Hello,
Unless you do a lot of doctoring of the Netinfo manager, EVERYTHING is going to try and go to the system partition. I have found that applications such as Firefox, that you drag and drop to the installation location, work fine. Make a folder on the Apps partition, and drag it over there.
Now, certain things are going to just simply insist on being on the System partition. Things that are hard-core Unix are especially in line with this, such as Open-Office, where it places hooks to things in the various unix directories such as /bin and /usr and /usr/local and so forth. You can install them to the system, and then copy out the main application and stick it on your Apps partitions too.
For the most part, I have the big applications -- Dreamweaver, OpenOffice, MS Office, GIMP, and Ragtime running from the Apps partition. Unfortunately, a few utilities such as Stuffit require System locations. I guess you cannot completely win unless you doctor Netinfo to re-direct a lot of the folders.
Suggestion is to make the System partition a little larger, and just realize that some applications are going to force themselves to that location. You may be able to copy the "meat" from one disk to the other, and then remove the meat. Expirement.
Oh, If you do install some hard-core Unix programs such as OpenOffice to your Apps partition, it will make a bunch of small support folders on the root of the volume. Just leave them alone. MOve them out of the window or something to ignore them. The directory structure will have to be preserved.
Not the perfect world, but then again, by setting up different partitions, we are pushing the machines a little bit.
Christian