Well, first thing I can say is simply this: Don't worry about it. Using a looper to play with yourself (in the musical sense) is pretty far off the beaten path compared to most other aspects of bass playing, and it takes time to adjust to.
As you said, the learning curve of using a looper plays a lot into it - it's like starting on a new instrument. Over time, you will gain a better feel for what will and won't work. When I started with loopers, most of the stuff I came up with for the first year or so was pretty sucktastic.
The best piece of advice I found when starting the looping stuff was that it's a good idea to start the loop simple. A short groove, a chord or two, maybe even just a muted hit - use things that are easy to build on. If you put too much stuff into the original loop, you can't add too much before it starts sounding like a traffic jam. You can always add another layer if necessary.
For live improvising, the above is even more important because you want your material to sound like a song. The looper gives you the time to think about what the song is saying, where it's going, etc.
For example, if you started by looping a single chord, you could gradually add notes in that key to create a melody, and you could then add more chords to provide harmonic support. Once you have that in place, you could solo over top of that or use the other looper to do another part to the song, and then go back to the original later if it fits.
With the JamMan, you can also try using the slow fade-out function to keep building on the fly. This way, you get a song that never remains static, which is also cool.
These are just a couple of examples. The amount of ideas and possibilities with loopers are literally endless - it can be a bit befuddling at times, but it's well worth the effort!
Hope this is helpful!
