Looking into using a VPN but I am having a problem in how exactly they should be used.

I have been looking at using a VPN for general issues of privacy along with other uses such as torrenting, but I keep coming up to a problem. Can I use a VPN while using other programmes that could identify me via my email or other usernames, while still remaining relatively private and secure?

These identifying programmes are ones that I use regularly if not constantly such as itunes. Would I have to turn off all such programmes to ensure that I could not be identified? If so how do you guys use VPNs regularly without also using any programmes that could potentially identify you?

I understand that if you only use a VPN for specific tasks this could easily be done (such as for torrenting) but for more general use it seems like it would be difficult not to accidentally use one of these programmes or websites once in a while.