Sounds fairly similar to my setup. I'm using a Carvin BX1200 though, but looking up the R1000, it looks fairly similar in most aspects. I run my bass direct into the V-Amp, with it on L3, full range into the Carvin, and then use the Carvin's X-Cver bi-amp, running a Hartke 410 for hi freq, and a Peavey 1810 for low freq.
My band is hard rock/metal, I'd have to dig in to see my exact settings, but I've got a LOT of compliments on my tone. I started with a basic clean tone, like a1 or something, gave a decent bit of drive & a bit of gain, and started tinkering with the stomp box settings. Of the two main tones I use, one I've got a bit more drive and heavy on the stomp box (I'm wanting to think the 2nd one, but I could be wrong), because we only have 1 guitar, so it adds a little extra crunch, especially if the guitarist wants to delve into some lead. The other is just a touch of fuzz and flange, a little hotter on the mids, and heavy on the bridge pickup. I'm not using any compression on the V-Amp, using a little on the Carvin, and the EQ settings. I also use a Hartke bass attack for shaping, but even without it, it still sounds good, just lacks quite the punch (had a battery issue, and forgot my powercord for it once). Since you've got a similar deal, what I did was started with the Carvin and got a basic tone I liked, which is also a backup should the V-Amp go out for some reason, I can just plug into the Carvin and be right back in business. But, I built that first, and then set into tweaking the V-Amp. Just play around with stuff, the tutorials here definitely help finding out where all the hidden settings and everything are. That was my biggest thing in the beginning, just deciding to not be afraid of the stupid thing, and start messing with stuff.
