How do I make a transparent connection between 2 VoIPs?

To make the VoIP be a transparent connection between sites you will want to use the Autocall feature. If the calling side is a regular handset then the interface type will be FXS and then FXO on the side providing the dialtone.

For example:
You have two VoIP with extensions 101(FXS) and 102(FXS) on one VoIP and 201(FXO) and 202(FXO) on the other. You could set Autocall on port assigned 101 to Autocall 201 so when that port is accessed it just passes through the dialtone from the other side's port one. You could also have FXO on both sides as long as both sides are providing dialtone into the VoIP.