The effects loop is between your preamp and the power section, so after the tone "flavoring" of your head. But effects loops aren't typically made for stomp type effects, as there's usually some volume drop, and pedals need to have enough power to drive the loop. Some pedals will sound fine, but my general rule of thumb that has always served me well (esp starting off) is to always put stomp effects between your bass and your amp. It's just more consistent that way.
This is especially true with Markbass amps. For whatever reason their effects loops blend the signal to 50%, so you only get half of whatever effects you put into them.
Eat all your veggies. And don't bang the dillies.