read the pj64 FAQ to get the min sys requirements. If you have less then that it wont run, so dont bother. Pj64 has no virus' or anything, best emulator there is IMO, so it shouldnt hurt your comp at all...
the actual cpu managing is done by windoze so if u have a normal computer (read: not overclocked) it should be 100% save to let an n64 emu run for over 168 hours or so (but it will probably crash before it has run that long )
ps. 168 hours is one week that's why 168 u can replace it with any number like 1964 or something