2. Mentioned in the TPControl - BYOD How To guide: Things of Note and Tips section, you can still use available file slots on the device if you need to choose completely different designs i.e. you don't have to use the file served from the BYOD NetLinx master (which lives in its own special slot).
We chose not to use ftp because it assumes ftp is open/available and also requires additional username/password information. So, the transfer is all done via ICSP which means you do not need to worry about additional port security/availability. Also, the file retrieval only ever happens once for the device, for any BYOD system it connects to. The next time it connects, TPControl determines whether there have been any changes or not and acts accordingly.
To give it a go, you can run a trial license on your system - give it a spin here: http://www.touchpanelcontrol.com/products/system-license.html