That's the Cypress FX2LP USB microcontroller (I recognize it because I use it myself). If you're using the Hi-Speed USB transceiver, then you should really go with a 4-layer board. Without that ground plane right below the top layer, it will be near impossible to get the 90 ohm differential impedance that you want for the USB D+/D- lines.
http://www.cypress.com/?id=4&rID=34128 flat out states that 4 layers is required. It also states that controlled impedance is required, but in my experience you can usually get away without it, so long as you carefully research your fab's typical stack-up and work out the right width, space, and height.
http://www.cypress.com/?docID=25406 also provides more info on calculating the width, space, and height for the D+ and D- lines.
4-layers isn't that much more expensive; Advanced Circuits has a 66 each deal for 4 layer boards that I use quite often for projects that use that very chip, as opposed to the 33 each deal for 2 layers.
In regards to your actual question...use plenty of bypass caps, as close to the pins as possible. If you split the bottom layer to have VCC and GND, don't have a trace cross the split on the top layer. Keep all high-speed signals on the top layer because the via inductance can kill what fragile signal integrity a 2-layer board has.
Good questions.
1) Does REF_CLK must be routed without vias.
Whenever you see something like "must be routed without vias" without a good explanation, chances are that someone does not fully understand what is going on and just think that is a good idea.
One of several things may be the issue:
- Different trace impedance on different layers, which will cause reflections whenever there is a via.
- Reference plane problem, because the impedance between the power planes of the design is not low enough.
Both of these are easy to avoid and is good practice - often even required if you want to pass EMI tests, build a solid design etc.
So provided you do this, you can use vias without any issues. The faster the signals, the more careful you have to design the vias. I have previously written about how to design vias for 28+ GBps signals here.
2) Does REF_CLK need termination resistor?
Best thing to do here is a quick simulation with your favorite IBIS simulator - or have someone do that for you (sorry, these tools costs money - but are worth it).
If you have very fast edge rates, chances are you need a termination resistor if the trace is electrically longer than about 1/3 of the rise/fall time. Use simulation to be sure (unfortunately you did not provide enough information about your design, or I might just have done it right away).
3) Is 4mm difference in trace length @50Mhz acceptable?
Another good question. Look at the rise/fall times of your signal. If the electrical length of the rise/fall time is significantly longer than the trace length mismatch, this will work just fine. Actually it is a good practice not to overconstrain layouts, even though it is often possible to match trace lenghts within a very narrow tolerance.
Best Answer
Dedicating a layer for grounding is not necessary in audio. Ground planes are an RF technique. At audio frequencies, you're not worried about effects like currents leaking across the epoxy substrate.
I just built a dual-supply (+/- 15V) audio board with four op-amp IC's, like yours.
(It was originally going to be a single layer design with a few jumpers, but then I decided to go with a manufacturer that makes two-sided, so I rerouted it.)
The +/- 15 power rails are strictly in the top copper, and the bottom contains the ground traces (not pours) and signals. Thus I have no jumpers, and no vias that exist just for the purpose of routing a network to the opposite side. (But not that it would matter! A signal, power or ground trace having to go to the other side and back has no effect at DC or audio frequencies. Stray inductances of of vias and such are another RF consideration.)
There is a small exception to the signals being on the bottom: late in the design I decided to add a stereo/mono switch, and some of the traces for that ended up in the top copper.
The finished unit is very quiet, and the sound quality is terrific.
If you have a good, dual-voltage power supply, quiet, distortion-free audio mostly boils down to the choice of op-amps more than anything else (I used NE5532's from ON Semiconductor), avoiding extremes like excessively low or unnecessarily high input impedances, and good supply bypassing.