Normally as you progress through the booking it will be self evident on what combinations are available in each category, but depending on the actual train-set it can vary. It should be clear where you can select a multi - bed compartment for a smaller number (e.g. 2 in a 3 bed sleeper.)

Frequently the option will have a fee for under-occupancy. 

I have never heard of any configuration in sleepers other than bunks (except possibly some really supreme sleepers i.e. expensive). 

As a strictly personal view I have never been tempted to travel by sleeper - cabins are small, rarely en-suite, many have poor catering, even with a pass the cost for 2 is higher than a budget hotel, you miss the view and many sleepers have multiple stops as they shuffle carriages from and to varying stations.

Munich to Vienna is only about 4 hours so a mid afternoon departure will get you to Vienna for dinner or a morning departure get you there for lunch.

You can book reservations on tickets.oebb.at. There, just enter 2 persons, add the Interrail/Eurail discount for both and then look for normal tickets (do NOT use "Seat reservation only”). You can select a sleeper and you'll be booked into the same compartment if possible. You'll get a warning if that's not possible anymore.

But during the day it's a fairly short journey.