1. I wouldn’t worry about booking in advance to guarantee seats. The express trains that require reservations almost never sell out, and if one does, there will probably be another train that isn’t sold out in another hour. A day in advance is plenty for a day train and about 3 days in advance for an overnight train. Reservations are usually available up to 1 hour before train time (when they sometimes quit selling reservations even if the train isn’t full), so if you plan to take a train the requires a reservation and don’t have it, plan on arriving at the train station 1 1/2 to 2 hours early.
2. You can book reservations on-line, but the best way to book reservations is at the train station in Europe. Buying them from a rail pass seller or other on-line travel agency will at least double the cost and since reservations aren’t refundable even a minor change in plans (you decide to sleep in an extra 1/2 hour some morning) means they’re wasted.

3. You can either buy them all at once at one of the major train stations in Paris, or buy the one you need when you’re going to leave Salzburg before you leave the train station when you arrive in Salzburg. I would seriously look at buying the reservations you’ll need in Italy while
you’re in Salzburg as there’s often a line, sometimes a long one, to buy “just a reservation” in
Italy. That’s one of the reasons I usually don’t use a rail pass in Italy, since it’s so easy to buy tickets (which include reservation, if required) there.
4. Finally, don’t bother with a reservation unless the specific train you want to take requires it. Most trains Don’t require reservations, but the express trains between major cities and overnight trains usually do, so you’ll probably end up taking trains the require them for every leg of your journey unless you make an effort to take slightly slower regional and local trains.

The main one I am worried about is from Paris to Salzburg. This is around a 10 hour ride (overnight). I tried to book online and they tried to charge me $230/ticket (so $460 for the two of us). Shouldn’t my flexi pass allow me to make reservations for free?

Can I even make reservations with the flexipass? Or should we plan on just showing up a couple hours early each time? I was under the impression that buying the flexipass was going to cover our travel costs from city to city. Is it more like a base rate then we have to pay a ton more for overnight trains etc??

There isn’t a direct overnight train between Paris and Salzburg, thus you’ll be using 2 days of the railpass. If you haven’t already purchased you railpass, look at buying this ticket on-line from bahn.de (special fares as low as € 73 are available most days, although you may want to upgrade from a reclining seat to a couchette for € 89 or 99) and buying point to point tickets for the whole trip.

Your railpass will serve as your ticket, required reservations on overnight trains are extra. I would assume about € 28 each in an 6 couchette, € 38 each in a 4 berth and € 70 each in an economy double (deluxe double is same price if you have a 1st class railpass), plus you might have another € 5 each for a seat reservation for the part of the route that isn’t on an overnight train. Full fare, 2nd class, for ticket and reservation is € 175,80 each for a 6 berth, € 185,80 in a 4 berth and € 223,80 in a double. As I stated before, you’ll pay at least double if you buy your reservations from an on-line travel agency.

While you can usually get reservations up to an hour before train time, I wouldn’t do this as a general practice. It may take some time to find the right window or office, there may be a line, and the person in front of you may be making 30 different reservations — this can be pretty stressful if you really want to be on the next train, plus spending a couple of extra hours in the train station is not my idea of the perfct Eurotrip. Buy your Salzburg reservation when you arrive in Paris at the CDG train station, or if you can buy it at Gare du Nord when you get off the train from the airport.

Well we have already purchased the flexipass so there is no turning back.

I am still a little confused about reservations. Do I need to pay for reservations, or is it just a way to lock in my seat, which will be covered by my flexipass?

Your flexipass is simply another way to pay for your Ticket, it covers the base fare for the train. Some trains require reservations. Reservations cost extra no matter how you pay for the ticket. If you choose to take a train that requires a reservation, you should not board the train without one. Reservations are sold for some trains that don’t require them, but unless it’s a long trip or there’s some reason I think the train will be particularly crowded, I don’t pay for a reservation if it’s not required. If you’re using a 1st class pass, don’t bother with a reservation unless it’s required as 1st class is usually not crowded — Europeans seldom spring the extra 50% for a 1st class ticket.