with the APM project, the transmitter and receiver are paired up. you can buy these together, of just research a bit of what receiver works with what transmitter. then, the receiver will plug into the flight computer (APM) - there is a graphic for this, channel 1 goes to input 1... etc.. then in software, you set the channel ranges, channel inversion among other things.
if you choose not to go this route, you will need to capture the output of the receiver and somehow integrate it with other sensors, to correctly drive the motors. there are some products for this, or you can hack the receiver to get the 'sum' signal out of the receiver to be used later in the flight computer sensor chain.
More time you spend preparing, more easy it will be to build one.
So why wouldn't you make some calculations about the hardware first, to make sure will the thing even fly....