Effects loops normally run at line level voltage and are intended for studio rack effects. This is a lot higher than the instrument level voltage that most pedals are designed for. Some pedals cope with this, others don't. Unless you know the pedal can handle line level voltage, the best place for it is in the signal chain.
The other thing you need to know is whether the loop is parallel or serial. Parallel gives you a blend, usually 50/50 , of clean and effected signal. This may not be what you want, for example if you are trying to compress the whole signal. Some amps can be switched from parallel to serial (Markbass LMII and III can), some can't.