No stupid questions...
Yes, by ear. Start by playing your dry tone and then kick on an effect. Adjust the level as necessary. Kick back and fourth a few times until it sounds right.
Every bass, amp, effect, player tweaks, room, etc. are going to make it sound slightly different. A lot of different effects have some sort of level adjustment to compensate for these variances so it's not very different than using a standalone fuzz pedal for example. There is no harm in making them all the same level per say, but why not add that extra bit of tweakability? The manual tells you to flip through different pages to adjust the different parameters and Level is one of those. I don't know that it gets into specifics but I'm not sure it's really all that necessary either. It's pretty simple to adjust the level on a regular basis. I suppose if you're using a million different patches it could be a PITA to check each one. If you're out gigging you will need to adjust your amp volume and its tone to fit the room and then you may need to change around some of your effect levels during sound check. It's something that may need to be done whether you're using single effects or a multi effects unit.
If your Ibby is farty I would suggest to turn down the bass. Your either adding too much bass, pushing your amp into overdrive, or passing the capability of the speakers. I would dial in some low mids somewhere in the 200hz range. I would also look at new strings as they make a huge difference on tone IMO. A fresh set of rounds is a great place to start. You can mess with some compression as well but I don't have any recommendations on which to use with the B3. Your best bet is to pick one and play around with it to see how it sounds to your ears. I'd suggest playing with one of the preamps or EQ's to get you in the ballpark of what you're looking for.
As for a basic effect to get started with I'd say it depends on what you're after. Compression is basic but it can also be very confusing. I would suggest messing around with a phaser or chorus on some clean passages or some of the dirt choices. Play with the 4 stage Phaser or the Big Muff. If you want a meaner sounding distortion check out the Rat clone (I think it's called the Rodent or something like that...)
With all that said, effects very well might not be your thing and that's perfectly okay! It's also possible that the B3 isn't your thing. It does a lot of things pretty well but it's not the end-all-be-all of effects by any means. I love mine and have used it regularly, but given the choice I still prefer my singles.
/superlongpost