Spend a few hours finding the tone you want. Adjust the presets on the RP150, don't use the ones they give you.
I have the same modeler and it can sound good. The distortion presets really suck. You have to make your own. Typically when recording a heavily distorted guitar, you will want to use about half the distortion or gain than you would when playing live.
Once you've dialed in exactly what you like, retrack your guitar parts. Don't try to fix it with EQ or anything. Just do them over.
[Edit:] I just reread your post. Yes you should record your guitar through the modeler with distortion. Just so long as you have the tone you like. I do it all the time. If I find it doesn't sound exactly how I like during mixdown, then I'll redo the guitar part.... and this is coming from a guy who hates retracking stuff. But that doesn't happen often because I get the sound I want before hitting the big red button.
I rarely ever EQ my guitar tracks except to lop off the low end.