There are two ways to program the boards Dave. The serial way, using a serial FTDI board which uses the internal bootloader program thats installed in nearly all arduino chips.
The bootloader runs on power up and waits for serial input - anything up to 5 seconds in some cases.
This is a Bad Thing. During this delay your board is doing nothing, its not producing PPM as your encoder
program doesnt run until the bootloader times out. Three reasons why this is bad:
1) All my encoders use 'power-up with stick thrown' for reversing. The bootloader delay means that by the time it passes control to your encoder, you may have tried a stick to check for servo movement, and so the encoder sees an unwanted 'reverse' command.
2) Powering-up some modules with no PPM present causes disastrous problems, Corona for example defaults to channel values way beyond the standard servo limits, which drives all the servos to the end stop and then strips the gearbox.
3) a transmitter that doesnt start transmitting until after some arbitrary delay is just a poor show. Say you catch your neck-strap and accidentally switch off during a flight. You notice and switch back on in time to save the day, but your transmitter doesnt start up until possibly 5 seconds later - definitely a Bad Thing.
The second way is to use a USBASP, this programs the chip directly via SPI.
With this method your encoder code runs immediately on switch-on, with none of the above problems,
and so is hugely preferable. Serial is ok for experimenting, but I would always suggest a USBASP and SPI.
There are many USBASPs listed on ebay, mostly 5v which is what we want, some also have 3.3v capability, some are 3.3v only, so check what you're buying. It connects to the 6-pin header on the Strong board.
Most of us dont actually fit a header, we just wedge one in temporarily whilst programming
Cheers
Phil