Like the other said, just make your reservations by going into the train station a day or a few days before your trips. You'll show your pass (though, they won't mark anything on it) and you'll pay a small reservation fee each time.
When you get on the train, a guy will come by to each passenger and will ask to see your ticket/pass. Show it to him and he'll have you mark the date on your own pass.
Once you mark a date on your pass, you can travel on trains as much as you want for 24hrs.
As far as France to Toulouse via Bordeaux, I believe the answer is yes. From Paris, you can get to Bordeaux on the TGV in about 3.5 hours (this is a fact). When you get into the train station in Bordeaux, just take a couple of minutes to reserve your seat on a train to Toulouse (I believe it's just a couple of hours away).
Lastly, in general, since you're traveling in September you'll have missed the big tourist summer rush that happens mostly in July and August as people have to get back to school and work, usually the first week of Sept.
Trains and planes won't be as busy then, but still make the night reservations in advance when you're clear on your travel dates.
I don't believe you can reserve your seats online since you'll be holding a special paper ticket with a designated time period you can travel and they need to physically see it.
Hope it helps
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