Setting up a secure VPN

I'm looking for info on the most secure way(for a home/home office user) to remote into a Quickbooks or other database based software "Server".

Specific example:

I have a client who owns two gas stations. He has a PC at his house. He would like to be able to remote in and use Quickbooks in all 3 locations and also share files, and use other applications that are specific to his industry(SQL based inventory software for example).

In theory I should have a PC at his house with a Cisco router, a PC/cisco router at location1, and a pc/cisco router at location2. They should be set to only tunnel into each other. Want this to be as secure as suggested. VPN, SSL? IPSec?

Also should be be using remote desktop software, or just mapped network drives? VNC? RDP? Service like LogMeIn?

I hope this all makes sense. I understand the theory(i think) but just don't know how exactly to implement! Used RDP/VNC/LogMeIn before but really for my own personal use and other's personal use.

Thanks!