I think it is save to say that it is a good practice to do anything you can on the ground rather then doing it in the air.
My setup: I usually end up with a similar set up as you do, though I don't use GPS much, but prefer hopping from one VOR to the next ;) (Well, I'll have to add that I'm not the most experienced pilot around here, for sure!)
Basic principle: I try to follow the rule I mentioned up there: I try to decrease the workload in the air by doing it on the ground already. That's why we make our route up on the ground, not as we go (well, one of the many reasons).
Let's say I have Com1 and Com2, each with a standby frequency as well as two Nav's, also each with a standby frequency: Before taxi, I'd have Com1 Active set up as tower and be listening and talking to Com2 to clearance, having ground in the standby. As soon as I have my clearance, I can put in my initial heading with the heading bug (not flying SIDs), as well as the Dep. frequency in Com1 Standby. This way I have all ground related stuff in Com2, all air related stuff in Com1. As for the Navs and the OBS: If there is a VOR at the airport I'm gonna put it in Nav2 and turn the OBS to initial takeoff heading (mostly runway heading). This is just as a support, "heading" still means pointing your nose to where the controller says, no matter what track the wind makes you actually fly. But then I know where I'm at and can already figure out what the wind is doing on my climb out. Nav1 goes to my first VOR, and depending whether I go direct or join an airway, I center the needle or set the OBS to the airway track respectively. The standby frequencies of the Navs are set to my second waypoint on Nav1, and whatever I think I'll need afterwards on Nav2. After takeoff I use Nav1 primarily to navigate, and Nav2 to verify my position (such a aircraft would usually have DME, so that you don't need to cross bear your position with two VORs, but if there is time to do so, why not).
In the air I usually don't use the standby freqs much on the Coms, and just swap Com1 and Com2 when changing frequency. Before landing, the same thing counts as before takeoff: Take as much workload off in advance. Thus I'm setting up the coms (I got 3 spare frequencies when talking to approach or center or whatever, the'll all be filled in with usefull frequencies like ATIS, Tower and Ground), the Nav's for the approach (with missed approach in standby if available).
Well that was quite a novel, I hope you didn't fall asleep halfway through. This is what I do, and I get along with it quite well. I am not saying it is the 100% perfect thing to do, and (as Simon points out in his answer) you should do whatever you feel the most comfortable with.
Summing up, I think doing as much as you can in advance is key in flying (especially IFR), as it gives you more time in case you need it for something else to do.