I sketch out individual room flow charts first. Then sketch out distributed wiring. Then I'll throw together my remote control notes. Next, I'll retrace the flow charts and remote schematic to look for bugs and verify operation. Then, lastly, I'll put together a finalized version of the project.
There are a number of illustration programs out there. Illustrator is great, even excel or power point have the ability to create flow charts. A commonly used pro tool is Visio.
You'll be able to find some open source alternatives around.
When I built my home years ago, I printed out multiple floor plans. One for security wiring, one for Russound and speaker wiring and one for data and av wiring.
I then had a spreadsheet that I made that I assigned a number to each cable and labeled it on the wire itself, in the spreadsheet and then on the floorplan. The spreadsheet listed the cable type, color, room, which wall it was on and then a field for any notes.
Seemed to work out pretty good for me and I still use it for reference.