Generic pin headers are in the "pinhead" library. For something like the breakout board with multiple rows of headers, you can just place them in the proper locations on the board layout.
That said, do you even need to create a PCB? Since everything is on .100 inch centers, you could just get a protoboard, and solder your connectors on with point-to-point wiring.
If you want to go to the trouble and expense of making a proper PCB, you may want to consider starting from the Fio design files and integrating the motor driver on-board. The connections will be more secure, and you will save the mass of the extra PCB.
In answer to your questions,
Remove the third lead, this will let you clear/prepare the pads for re-soldering.
It's probably best to flick the old solder off the leads; do this by heating and bending the lead with the tip of the iron and letting it spring back, DO NOT DO THIS TOWARDS YOUR FACE!
You can buy solder with a flux core. Also, if you can get it, buy lead solder, it is MUCH nicer to work with.
As regards the vid:
Yes the guy tins his iron to remove the leads, you should always tin (add solder to your iron tip) before you do anything, it stops the tip oxidising. It also helps when melting old solder.
To clean the pads generally I would put a bit of new solder on, then wick it off to give a nice clean and shiny surface.
He is applying flux, this will stop the solder "balling up" and sticking to stuff it shouldn't. You can do this, but if you are careful, and have flux core solder, you wont need to.
As regards the rest of your questions, this is just about technique. The guy seems to tack solder (a connection made to hold it in place) the leads at first. When the whole lead is tack soldered he goes around and tidies up the job.
So what YOU need to do.
Remove the lead - Tin and clean the pads and flick the old solder off the end of the lead (NOT TOWARDS YOUR FACE!)
Add a little solder to each of the pads
Place each lead above the pad and push down gently whilst touching the tip of the iron to the solder you placed on the pad. Make sure you remove the iron before removing the pressure.
When all connections are made, get some tweezers and push down on each lead in turn, melting the solder on the pad with the tip of the iron so the lead is properly flat on the pad.
Remember! Before you touch the iron to anything, make sure you have applied some solder to it and wiped it off on a sponge.
Also, if you are buying new equipment, when you first turn the iron on, keep adding solder to the tip and wiping it off. You need to thoroughly tin/protect the tip before you start using it. You can get little pots of hard flux, this is useful and it will help remove the crud on the tip due to oxidation. Also, tin it and DON'T wipe it off when you are done, the tip will still be hot for a while after you switch it off.
Best Answer
I typically use the footprint for a 0.1 inch pitch "pin header". You can then use either male or female connector strips, or just solder wires directly to the pads if you don't need to use a connector. But using the header/connector provides a convenient place to show where the external connections are in the schematic and on the board. But it does not compel you to actually use connectors (or headers) if you don't need them.
If you want to use connectors, the male pin headers are available in strips of ~40 pins and you can just snap off however many pins you need. And you can make female connectors (with however many pins) yourself. I find it rather compact, convenient, and low-cost solution.