Assuming you get comms to the new gateway then you can program the installation list, it brings up all the possible installed modules and you simply tick the ones that you know you have.
Most will be obvious, some may have several choices and you might initially pick the wrong one, you may also miss things that you should have included, but as long as you get the important things like engine ECU, instrument cluster, body control module etc enough vital systems will be talking to each other for the engine to start and run, doors to lock/unlock etc.
Then its a case of looking at the fault codes for comms errors/module incorrectly programmed etc and working out which installed option you should have ticked, it won't look for things that you have not told it are installed so if for instance you have a Bluetooth module it won't be working but you wont see a comms error or anything, you will then need to add it to the installation list.
I chose the latter as its something I have which I have disconnected and deselected from the installation list as it was bringing up comms error codes.