I see that kids are free to many places covered in the Paris Museum Pass, but will we have to wait in line to get them any type of "free ticket" to enter or can they just walk in with us in the special lines?
You won't need to get them a special ticket. The nice thing about traveling with the kids in Paris is that you can usually go in a special line or entry point. At the Orsay, you go to the right hand side of the museum and they will let you in! If you decide to go to the top of the Arc de Triumph you can ride up the elevator instead of walking up the stairs.
My kids adore Paris and can't wait to go back again! Have fun!
The kids just walk in with you but my 16 yo son was asked for proof of age of couple of times because he could pass for older. Otherwise, you just say "etudiante" as you go through the line.