Yes, what you make master and slave, and what bus you use for what is not really too big of a deal at all.
Cakewalk likes to install on the same physical drive as your OS. Let it.
Once Cakewalk is running, most of the app is in RAM, so not really an issue about the OS wanting to go back to Cakewalk for info while it is doing a process.
But, where you have temp files, and also where the .wav files you are working on, and how the OS likes to do other things in the background can be an issue.
Here is a decent solution. Install OS, Cakewalk on primary drive. Record to the other drive. Create temp files on drive other then where the.wav files are stored (basically on the same drive as Cakewalk, just use a different folder). There you go. Also, save the new files that were processed on the same drive that the original .wavs were on. Basically, it is going to transfer the temp file one on drive to a permanent file on the other drive. A fast process.
Man, there are so many issues here, as there always is with hard drive recording.
Oh yeah, let the plugin's install where they default to. I have always had luck this way, but when I have tried other directories, have had problems. Usually the plugs will list themselves with any software that use them without any problem. If they don't, well, there are probably some issues that a software patch deals with. Check all the vendors sites for these issues.
Ed