Here's what I was taught from a book somewhere. Not that I'm anything close to being an expert.
1. Needle down, Needle up and pull up the bobbin thread. If the bobbin thread is left below, it can become all knotted up in your FMQ stitches.
2. Make a couple stitches in place to secure the threads.
3. Here you can do a couple of things:
a. Just clip off near the fabric. (This is what I normally do.)
b. Or, leave a tail and use a needle to hide between the layers.
At the end of a row of FMQ stitching, I just do the reverse. Step 2, step 1 and then step 3.