Just a couple of tips really, that have helped me in the past...
MIDI bass guitars can sound a bit fake (some are absolutely fantastic), they just try to hard, a way round this is to use a Double (Stand Up) bass instead, it can sound much better, even on Rock numbers it sounds pretty OK.
Why does it sound better? well partially because of the muting, many double bass emulations have a fast decay, they are trying to emulate a great big piece of wood, and that doesn't ring for very long.
Therefore another simple way to make a electric bass sound great in a mix is to mute it, some bassists constantly use a palm mute, but it's really much easier for a whole song if you just stick a little strip of foam under the strings right by the bridge, so it's just, touching, you'll probably need to trim it a few times, I wrote BASS MUTE on it so I don't chuck it away.
Tony Levin used a nappy as a mute when he recorded his bass on Don't give Up for Kate Bush and Peter Gabriel...
Try it, it does make the mix much cleaner.
Hope this helps