...so now I am wondering the best way to make reservations for a sleeper can on this train.
The problem here is that MAV website doesn't sell online sleeper reservations separately, but only ticket+reservation as a sort of combination, thus there is no possibility to buy a reservation itself to compliment your pass
So I am wondering, is it even possible to reserve/buy tickets online, or is it something that needs to wait until I land in Czech and go to a travel agent at the beginning of my trip?
As we see it, you have three options here: a) some of the agencies (including those located abroad) besides passes also offer issuing sleeper reservations. Obviously it will be more expensive in total (comparing to what you'll pay in Hungary), but in case your company pays for everything that might not be an issue. You can either ask from the agency where your pass was bought or just see Eurail Group page
(under 'How to I make seat or bed reservation...') for the list of official sales agents; b) don't bother with all those agencies and just purchase your reservation already in Prague from Czech Railways (CD) international ticket counter, they should be able to sell it to you for the same fare as in Hungary; c) or even buy it already in Budapest. There are two direct overnight trains and doubt that everything will be sold out far in advance. Generally there is no problem to buy a reservation even on the day of travel (for instance for today there are still double and 3 bed sleepers available)
Just as info, sleeper reservation fares: 3 bed sleeper (28 EUR in trains 'Ister'/'Muntenia' or 32 EUR in train 'Dacia'); double sleeper (42 EUR and 43 EUR respectively), DeLuxe double (60 EUR for all trains); single sleeper (98 and 99 EUR respectively) and DeLuxe single (110 EUR for all trains), while in agencies it will be slightly (or maybe even more then slightly) higher.