Kemper user here - and I'm very pleased with it... - like with all multiamp type things, it's always a challenge to get a consistent sounding rig, especially when using lots of patches and effects. How do you get it right? well..... that's what rehearsals and lots of gigs are for...
However, there are a few things to watch out for and may help you.
EQ - for example cutting your mids is going to make you sound weaker in the mix. People also have a habit of whacking up the bass control... that bass control is generally not your friend if you want deep punchy bass... you'll soon end up with a load of mush, especially in a band situation. This leads on to...
Compression - (especially multiband), can help you cut through and sit better in the mix than without
Volume - getting your patch level consistent is imperative. You can check this by playing a loop back through your settings into a DAW and watch the meters. (Of course, the above two still need to be taken into account - just cos they meter the same doesn't meant they are the same!)
Here's the secret... record your band with a multitrack capable desk. Playback the set with your dry bass sound going through your modeller. Then, you can tweak your setting on your modeller to your hearts content until it sits right with the rest of the band.