The thing is that you're seeing things with a Windows perspective ("primary drive"??????) and OS X is a Unix system. There's only one directory tree and any volume hangs off it. There's no C:, D: and other such sh-!-t. The boot volume, from which the Mac started up, mounts at root ( / ), and any extra volume such as your second partition or any USB flash drive will be automounted off the /Volumes folder. Applications reside in the /Applications folder of the boot volume and most expect to be there in order to run correctly.
If you want to have VMware Fusion available on both systems, you will have to install on each, since that app comprises not just the main package found in Applications, but a lot of support files spread out elsewhere.
Personal items such as bookmarks are stored in the corresponding subfolder inside your account's home ( /Users/YourAccountID/Library/...). Each boot volume has its own user directory and, hence, each has their home folder. On top of that and for security reasons, the keychain is tied to a specific volume: if you copy it over that invalidates the file and makes it unusable.
You ought invest in David Pogue's Missing Manual books....