Hi,
Disabling Restore Points etc.. right click Computer -> Properties -> System Protection
Set to "Off" on any disks presented down there.
Re. backing up. If it is just one program then yes it would be good to backup that specific data on a regular time and then occasionally make a backup of the whole virtual machine package. You can use normal windows backup software for that specific application and backup to a location not local to the host. Eg. backup to an external disk or external network location.
In regards to using a shared location for putting your data. If you are talking about VMware Shared Folders I suggest to not do that. While it can work for some scenarios there's plenty of problems with it for not using that from both guest and host side. The general idea is good, but the supplied feature just doesn't cut it at this moment for that particular usage. It is good for file exchange between guest and host, less suited for actually working on documents presented to that share.
In that scenario I would suggest to use industry standard network sharing (CIFS or samba/NFS/..)
I am guessing that your aim is to depend on Time Machine for backing up that data. Beware that Time Machine cannot make reliable backups of your virtual machine and that you should exclude the VM from TM.
It is fine to pause/suspend the guest OS if you plan to continue working on where you are. I do that frequently.
If however you want to make a backup of the virtual machine package then you best shut down the virtual machine using the normal controls in the guest OS (eg. choose shut down from the start menu in Windows 7) and then when Fusion is shut down as well you can make a reliable copy of the guest OS package.
hope this helps,
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Wil