Do we have to submit a Paid Application Agreement if I intend to fix a price for my app @ 0.99$
Yes, you have to submit the agreement no matter what the price is - as long as it is not free.
The agreement runs for a longer period, but Apple will periodically make updates and changes, and at that point you'll have to agree to it again.
You can update the pricing at any time both before it is listed on the App Store, and while it is listed on the App Store.