You're right that there are better places to post your question. The section you picked deals with the TIme Capsule hardware. Your question involves the Time Machine software, best dealt with in the discussion section for your version of OS X.
By the way, you don't seem to have declared any of your system details in your profile or didn't select your details to be included in your post. Those can help people give you correct advice. To update that, click on "Your Stuff" near the top of a window on these discussion groups, then on "Profile". Scroll down to "My Products" and either edit an existing one or add a new one.
Regarding your question, it's easy to exclude a VM's "virtual disk" from Time Machine backups using the "Options" button in the Time Machine panel of System Preferences. As you recognize, that leaves you without a backup of that VM unless you can back it up some other way. One way to do that is with a separate external disk drive. You can just drag the VM file to the external disk drive whenever you want to back it up. Depending on how you do that, it will only keep one copy of the VM. If you want to keep more than one copy and you have room on that external disk, you can create folders on the external disk to hold more than one copy of the VM.
