If the repeater talk-in frequency is 5Mhz higher, that is a positive shift. (A negative shift is that the talk-in frequency is lower than the repeater talk-out frequency).
PL tones are up to the repeater's owner and there are no hard and fast rules. I've seen some who use a PL tone for talk-in but not on the primary output. I've seen some where PL tones are used for both talk-in and talk-out. Where PL tones are used on both, they can be the same or different. (Some times talk-in and talk-out are different just to control who is using the repeater, but any ham worth his salt will figure that out in a matter of minutes).