I will be traveling from Vienna to Krakow, and there is only one train that runs anywhere in the timeframe I need. I have been on the OSS Austrian Railway site and Polish Railway site and cannot find anywhere to reserve the tickets. Does anyone know if/how I can do this online, or will I have to buy them when I am there? If I have to buy them while there, what are the chances of the train being full?
You don't say which time frame you need, but there are two Vienna-Krakow trains that offer SparSchiene fares, one that departs at 14:33 and the other (a night train) that departs at 22:33. See here. You can book either of those trains by phoning the Austrian Rail call center. I think you should be able to book earlier in the day standard fare routes the same way. Dial 011 (US international access code) + 43 (country code for Austria) + (0)5-1717. Omit the zero in parentheses. It is only used for calls originating in Austria.
You may have to buy tickets in Vienna. Go to the RR station and buy them as soon as you land. I have never reserved in advance and never missed a train.
I learned early to ask everyone I saw on the train if I was on the right train to my destination and if I was in the right car. Those vary on European trains; so be careful.