I use a Boss CS-3 compression pedal. I used to use an Orange 100BXT bass amp which has no built in compression so that was straight forward. I have recently bought a Eden E300 mini stack. The amp has auto compression built into it but I still like to use my pedal along with it because I get sustain with my pedal and don't with the amp on it's own. Is this okay?

Using two stages of compression won't hurt your amp or anything, you might just have a mixture of sound a bit. For sustain, there are sustain pedals for keyboards, so you might be able to use one for guitar... depending on what model it is. You would probably get way better compression out of the Orange amp than the compression of the Boss pedals because, well, Boss is not much of a boss brand when it comes to gear...