Just to let you know what lies ahead....
If you want to go from making a hand-built breadboard or prototype to actual PCB's, you have a lot of hours and anywhere from several hundred to a few thousand dollars cost in front of you, depending on how much you are willing to do yourself.
Schematic capture and PCB layout
First of all you need to capture your design using some sort of schematic capture program, and then design a PCB. One of the more popular programs is EAGLE, which I use. They have a EAGLE Light version ($49), but it can only be used for schematics with one sheet (any size), two signal layers, and 100x80mm (approx 4"x3") routing area. For any serious work, you need at least the EAGLE Standard version, which costs $747. There are probably other less costly (even free) alternatives. There are lots of others that cost thousands or tens of thousands of dollars. In any case you will have to spend considerable time learning how to use the program.
Or you can pay someone like me to do it for you ($$/hour).
PCB Fabrication
Getting boards made is the next step by a PCB fabricator. The problem here is the NRE (non-recurring engineering) costs. Some board houses treat this as a separate figure, and others built it into their per-board quote. In any case, it is almost never economical to have just a few boards made. You might spend $100 for two boards, and $500 for 25. You need to have really large quantities to get down to just a few dollars per board.
The gotcha is, if you make 25 boards, populate just a couple of them for testing and find they don't work (and there is not an easy fix -- e.g. because you laid out a connector backwards), you might end up throwing away the other 23 blank boards away and you would have been better off just getting two. I have stacks of blank PCB's as evidence of this phenomena.
PCB Assembly
Unless you are willing to build the boards by hand, you will need to have them assembled. Surface mount packages are difficult to deal with. If the board has BGA or QFN packages, you probably won't be able to build them yourself unless you have your own reflow oven.
Getting your first two boards built by an assembly house might cost $500. Whereas getting 25 built might cost $1200. (Once again, the problem here is the NRE costs.) Getting down to just a few dollars per board requires (again) large quantities.
And someone else has already discussed the problem of getting parts.
Make sure you use parts that are readily available -- if both DigiKey and Mouser have hundreds of the part available you should be okay. If instead, they have it in their catalog, but it is currently out-of-stock, try to find something else. If you need some special parts that aren't carried by DigiKey or Mouser, make sure you have a reliable source before incorporating it in your product. (Note: the more unusual parts you use, the more likely you will have to add the part manually to your PCB parts library.)
Custom Cases
Do you want to put your board into a case? If you need to have a custom case designed, that will be a couple thou for the designer using a program like SolidWorks (I don't do that, but can recommend someone who can). If you are going to make just a few cases to begin with, you will probably need to go with rapid prototyping, such as Selective Laser Sintering (SLS). Figure at least $100 per case in small quantities. To get down to a few dollars per case cost, you need to have a custom mold made. NRE time again! Plan on spending $10,000 or more for the mold.
And I won't even start on EMC or EMI testing, since I don't know if it applies to your product.
As you can see from all of this, until you get into production, the cost of the electronic parts is usually not the biggest item on a per board basis. Doing your own assembly for small volumes will save you a lot of money. So it is important to design with that in mind -- no impossible to solder-by-hand parts.
To get really low prices for high-volume, generally you need to go offshore -- China etc. But I would avoid doing so in the beginning.
You'll typically want to panelize boards made for machine assembly. Loose boards are going to be more expensive to populate because special fixtures have to be manufactured and used (unless it's got really wide unused areas on the sides), and because there is more handling to populate (say) 12 single boards than a 4x3 panel.
That means more up-front NRE and tooling costs and more per-unit cost, which is pretty much the general result of not following guidelines.
You should put adequate tooling strips on the sides (typically 10mm bits that will be snapped off and discarded), tooling holes on the strips, and fiducial markings at least diagonally opposed on the tooling strips (for alignment), and diagonally about any high-density BGA footprints. You can see the fiducial marks (dots) on the tooling strips below.
Here is an example of using "mouse bites" and routed outline to allow such a PCB to be depanelized with a minimum of drama:
The board can be snapped along the lines with close-spaced (unplated) holes, leaving a smooth edge most of the way around. (the image shows a couple of ways of making the outline, but typically you'd need an additional routed line or V-groove to separate the boards in the other dimension).
I prefer V-grooves alone to mouse bites for volume boards, but it tends to cost a bit more, and they must extend all the way across the panel, which can be limiting. You have to pay attention to the stiffness of the panelized board assembly or it can cause problems in the assembly operation (so you can't cut too much away on a thin board).
Sometimes you can put test coupons for controlled impedance, wiring to power boards for testing or other disposable circuits on the tooling strips.
You'll want to minimize the setups and operations. A relatively small number of different SMT (only) parts only on one side of the board with adequate spacing should be cheaper for machine assembly. Anything that cannot be supplied in a tape and reel with a proper leader will cost more to assemble.
Minimize the number of different parts on the board (there are only so many part feeders on a P&P machine- 25 to 40, perhaps). It may be better to use a few more of the same part or otherwise rationalize your use of parts (if you need a 4K7 resistor for an analog circuit, maybe pick that for all your pullups, if you are using a zillion 100nF/10V ceramic bypass capacitors, try to to use them in other locations.
Much more could be said, and the illustrious Australian Dave Jones has some good videos on the subject- he was a professional PCB designer and has worked for Altium, so they're quite good if you use Altium. (often you can get the link from the right sidebar in SE) Altium has good built-in tools for panelization but, of course, you have to know what dimensions you want to use for the panel, spacing, route widths, allowance and copper-pull-back around V-grooves, fiduciary marking dimensions etc.).
Some of this varies from manufacturer to manufacturer, but there is a lot of common ground. Don't make the panel too big to fit in the assembly machine(!), something around 9 x 12" or thereabouts is usually fine for modest size individual boards.
The board itself should have adequate spacing between the parts, preferably no parts hidden under other parts or on the bottom of the board, proper pad dimensions, and unplated holes where desirable. Slots should be used instead of huge holes if through-hole parts have flat leads (eg. barrel connectors). Hole sizes for through- hole parts must have adequate clearance to account for tolerances or they can't be reliably machine-stuffed. Bigger is better (up until the point where soldering is compromised). If you need to cover bits for wave soldering (so holes won't get filled in, or connector tabs covered with solder), you need an additional masking or taping step. Parts that require alignment (through-hole LEDs, for example) can require custom jigs or fixtures, for which you might have to make allowances on the PCB.
Best Answer
1.) Order your flash pre-programmed from your supplier. Usually you can use JTAG to reprogram on the line if things change. Or maybe an ISP header connected to the flash lines if you don't have the JTAG option.
2.) Yes. Especially for smaller runs, or things that need more reliability. Sometimes with high volume consumer products you either test samples or do a simpler test. I'm a little obsessive so I usually have everything tested. At my US factory test time costs about $1/minute so I can afford it.