It sounds like you're looking for a VPN (virtual private network) solution. Filezilla is an FTP program which is not going to help you.
For my business needs I use Sonicwall routers
to connect networks together. Using this type of setup, you need to have at least one of the locations with a static ip address.
If you're looking for a free VPN solution, you could use something like Hamachi
, which I also use for friends and family. With the free setup, you can have up to 16 computers connected together. They have a pay version (about $200 per year) which allows you to have up to 256 computers connected. There are other vpn solutions out there, those are just the two that I use.
Once you've got your vpn set up, you can access systems like they are on your own network (just not as fast obviously <g>)