The distribution varies from country to country, but in general there are three classes of trains you may encounter:
1. Trains without seat reservation. This includes local and regional trains almost everywhere, and a fraction of longer-distance trains that varies by country.
For these you just board the train and hope to find two vacant seats close to each other.
2. Trans with seat reservation, but without surcharges for pass holders. In some countries, plenty of long-distance trains fall into this category.
Walk up to the ticket counter and say "we need two seats for such-and-such train". If the person at the counter asks whether you also need tickets, say "no thanks, we already have passes". You -- as well as travelers on ordinary tickets -- will often need to pay a (generally small) separate fee for the reservation.
Depending on location, it is often possible to buy the reservation from a ticket machine, which will give you the opportunity to select seats yourself. Try poking around in the on-screen menus to see if it offers that; if not just go to the staffed ticket counter.
In some countries many trains have optional seat reservations where you can choose between method (1) and (2) yourself, depending on how far in advance you're laying your plans and how much it would ruin your day to have to stand. If you choose method (1) you risk being bumped out of the seats you find by people who have reserved it; if you choose method (2) you risk discovering on the day itself that the train is all but empty and feeling that the price of the reservation was wasted.
3. Trains that require surcharges for pass holders. These include most high-speed trains and generally also require reservations in advance. Sometimes the number of pass holders on each train is restricted.
Walk up to the ticket counter and say, "We would like to go on such-and-such train. I have pass A and my friend has pass B. Are there any seats left you can sell us?"
Having different kinds of passes is no barrier to reserving seats next to each other, assuming that there are any free seat pairs left to sell at all. If there aren't, you'll need to choose between getting separate seats or traveling at another time. (Or, if you're feeling splurgy, asking if upgrading to 1st class and/or buying full-price tickets would help the matter).