We book direct through official disneyland paris pages. I have found booking with travel agent isn't that much cheaper, if cheaper at all. Plus when it comes to booking dining and other things I have had to do it through the travel agent, where by booking with disney I can do it myself.
As for flights, we just book ourselves with whatever low cost airline is offering the best price or flight schedule.
It is fairly straight forward to book and after being a few times I cant see what the travel agent does that I can't, hotel, park tickets and meal plan in disney booking, flights with easyjet and taxi transfer. Job done!.