Go out of the POD and straight into the Loop of your Amp! Use your Final signal in the Pod! Whether it´s Hi or Low Z? Balanced or not, Just match your Pods Out to what your Amp has to offer as the loops input!
Using Loonybin's suggestion, you would be using the Bass POD Pro entirely for the preamp (amp modeling) and effects going directly into the power amp of your Ampeg.
If you just want to use your Ampeg's preamp with the effects of the Bass POD Pro within the effects loop I would suggest the following:
Connect your bass to the Ampeg's input. Take the Effects Send from the Ampeg to the Bass POD Pro's Line Input on the back of the unit and set the front switch to 'LINE INPUT.' Then, take the left mono output of the Bass POD Pro back into the Effects Return of your Ampeg. Make sure to go over your Ampeg's documentation for any further settings you need to make using the effects loop.
I'm currently using the original Bass POD Pro with an Ampeg SVT 4 Pro bass amp and I've tried inserting the POD into the Ampeg's effect loop and while this is quite effective if you're only interested in using the bass effects from the POD (i.e. chorus, flange, compressor, octivator, etc), but if you wish to use the bass preamp modeling as well, then you'll find an awkward at best 'push-me/pull-you' struggle with your Ampeg's preamp section. I play a six string bass in a prog-rock band which requires a preamp tone that works well across multiple techniques (i.e. finger style, slap and pop, tapping, etc) yet the Ampeg's preamp alone does not provide this well, but the Bass POD Pro preamp modeling most certainly does. The only way I've gotten this to work well is to run my bass directly into the Bass POD Pro and then route the unbalanced 'model' output signal in 'live mode' (which removes any cabinet modeling) from the Bass POD Pro directly into my Ampeg's power amp input. Since the Ampeg SVT 4 Pro has a stereo/bridged mono MosFet power amp section, the best application I've found (and I'm driving two cabinets, a SWR 4-10 and a SWR 1-15) is to set the power amp to bridged mono routing the output of the POD to the power amp 'A' input on the Ampeg. This effectively makes the Bass POD Pro the preamp and the Ampeg SVT 4 Pro just a bridged mono power amp. I've been very happy with this set up and since I also use a four string fretless (and have an original line 6 floorboard); I can not only have different bass tones for things such as soloing but also different preamp tones for the different basses I use available with usually just a single step on the floorboard. This set up will work just as well without the floorboard, you'll just have to use the buttons on the unit itself for switching patches and to use the tuner (which btw works very well with five and six string basses). The particulars on routing the POD's output directly into your Ampeg's power amp section will depend on which Ampeg amp you have, but the point is, if you want to use the preamp modeling from the POD, you need to run it's 'model' output in 'live mode' directly into you Ampeg's power amp input. I hope this helped.