Where you place your looper in the signal chain is very important to the recording and playback quality of your ideas.
In my experience, placing the looper at the end of the signal chain of effects pedals will give you the best results and allow you to add effects to layered parts without those effects being added to your recorded material until you want them in the mix.
Bear in mind that any effect you use while recording will be added to the playback. You'll get to see and hear how this works in the upcoming examples.
If you choose to place the looper at the front of your signal chain, effects coming afterwards when selected will affect the entire recording. Tracks that are delayed or have wah added don't sound that great (trust me!), unless you're going for audio weirdness!