Personally, I would rather be closer to the airport, just in case there is some sort of delay. My choice would be Freising, which has a good number of affordable hotels and a 20 min bus ride to MUC.
However, if you prefer to stay in Salzburg, there is one regional connection and at least one express train connection to the airport every hour.
There is no direct train to the Munich airport. There is only S-Bahn service to the airport from Munich Hbf or Munich Ostbahnhof. Regional trains and EC express trains stop the Hbf and at Ost; RailJets only go directly to the Hbf.
I see an S-Bahn/Regional train/S-Bahn connection from Salzburg Hbf to MUC with connections in Freilassing and Ost, leaving Salzburg Hbf at 6:58, getting to MUC at 9:35, giving you 2h35min to make you flight. You can do this connection with a Bayern-Ticket, 28€ for two of you - no advance purchase required.
There is another connection leaving Salzburg Hbf at 8 o'clock, changing at Ost, getting you to MUC at 10:15, giving you 1h55min to catch your flight. With sufficient advance purchase, you can get train specific discounted tickets for two for as low as 29€, including (if you book it that way) the S-Bahn.