Not a problem. If a infection gets into the system restore system it usually cannot be removed by a anti-virus program or other types of spyware programs as they are protected by the restore sytem itself. I am not good at making backups for my system but there are programs that allow one to do that.
By purging a possible infection out of the restore system and then closing restore down you are then pretty much assured that if your pc contracts another type of infection that various programs ex: antispyware, Avast, and others would be able to find it and remove it from the system without worrying about that infection reappearing from the restore files after removing the infection from the rest of your pc. If the infection is contained in the restore system it will keep reappearing after you have removed it from the rest of the pc.
Hopefully there are others here that can give you more detailed instructions, links, examples of how to back up your HD information.