I'm running Milkyway@Home on my GPU and Seti@Home on the CPU. As i have no control over the scheduling between the two projects i know of, most of the time it doesn't work because BOINC gives priority to either Milkyway or Seti but never to both projects as it should be as they can easily run both.

Now my idea is to have two separate installations, so one can run seti and the other Milkyway and BOINC has no way to mess up my resources.

I think the problem will be the registry where the used folders are set, so the second installation will most likely overwrite the folders of the first installation.

Is there a version that doesn't use the registry?

I'm using Vista 64.

BTW are there any plans to make BOINC usable again? My impression is that it gets worse with every new version. When a new version comes out the workarounds that didn't work well with the previous version don't work at all with a new version. The problems from the old version aren't solved but new problems were introduced, so i need new workarounds for the old and the new problems.
The last days i had to babysit nearly every new WU. I have to trick out every system i set up to run BOINC because of every reason one can think of and because of some reason you even can't.

Isn't it possible to make a simple version that i can set up for every core separately without any user account messing that simply allows control over the science apps.

I'm really annoyed and understand very well everybody who leaves BOINC - i'm thinking of leaving more and more and i really like the idea of BOINC.

CUDA is quite new to the DC scene, and it will take a while to get the hang of how to make it 'play nicely' with the cpu in BOINC applications.
Using the GPU as a BOINC cruncher isn't as wonderful as a lot of people like to make out it is.

A far simpler way of doing what you want, is to have one computer only run SETI, and another only run Milkyway. No messing with the registry, no fiddling with preferences, just straight forward 'set and forget'. At least until one of your projects changes things and you don't know about it.

Milkyway is not cuda. If Seti could do ati, i would run only seti. I have hosts running only seti on cpu and gpu and there's nothing straight forward, it's the same bad game only other players and actually working workarounds as it is with other hosts running only seti cpu.

so your solution sadly isn't far simpler, it's simply impossible for what i want.
I want to run seti as much as possible and other projects(Milkyway) where seti isn't possible(ATI) and BOINC does everything to make it hard for me, regardless if cuda, ati or only cpu.
From 9 hosts there is only 1 old notebook that actually doesn't need any tweaks to run BOINC and there are only 4 hosts with usable gpus.