I need to connect to a webservice which is behind of a VPN
via PHP. My server is Debian Linux (Squeeze).
From PHP point of view, the VPN is just a plain network connection. It does not require additional handling.
If you want to dynamicaly estabilish a VPN connection, you'll probably need to use exec() and some commandline tool for estabilishing a connection. But as such connection doesn't interfere with normal network communication (as long as it's properly configured, with other subnet ip range), you should estabilish it once and keep it active for PHP and other apps to use.
VPNs are at a network layer below PHP, PHP won't know or care that the connection is over a VPN or a normal connection. It's handled by the network stack.
If you use a permanent one (e.g. IPSEC) then PHP doesn't need to create the connection, it's just there to use when PHP connects to an IP address that is in the VPN. It is selected to use by the network layer when it does the routing, not by PHP. This is true even if you create the VPN on demand, as jderda suggested using exec() or similar. But a permanent connection is better (IPSEC).
So to answer your questions: