I think that the bus to Basel airport from Freiburg goes to the French side of the airport. I need to check-in on the Swiss side. Does anybody know how to do this?
For most airlines, you can check in on both sides of the airport.
The only exceptions are British Airways and EasyJet. For these two airlines there is only a check-in on the Swiss side.
When you arrive by bus on the French side, you can cross the "border" into the Swiss side in the departure hall on the 3rd floor. You need a passport or ID.
....... and either an airline ticket (which you will have) or car hire documents.