I currently have to use ARCServe also, and yes it is un-user-friendly and a POS... However, it will do backups simply, once you get it setup. It will do exactly what you are describing. If the main interface is too cumbersome, just use their "Wizard".
If you have the space, you could do full backups every day of the 6 folders you require, Monday-Thursday, then have rotating full Friday backups, for each Friday of the month, 1-4 or 1-5, then you can go back in time to restore. The same can be said for monthly backups. Like I said, much of this depends on how much room you have on your backup media.
In regard to backing up the whole server, I would make an image of the server using Ghost or something similar. Keep your images up to date after major changes, and test them, if possible.