I find the 5.5mm charging cables on ebay (You can also make your own from type N-ports from Radio Shack) you have to sometimes buy ten sets at a time, but the are SUPER cheap. I get mine for $9 shipped and then give the others to people I know who are building packs.
This is how I set up mine -
You'll notice that I have a kill switch between the board and the battery. I do this so that I can isolate the electronics while I am charging the pack. It also acts as my main kill switch for when I am not using the pack.
You will probably want to extend the wires from the charging port to the cable going to the battery. I tend to put my battery up high.
I also attache my battery with 3M foam tape. It sticks great (two years on my last pack and no problems) and is a simple clean way to mount things to the motherboard. I got this idea from Spongeface and is now the only way I attach electronics to the motherboard.
Hope this helps folks!