You should be fine with your original reservation as long as you are keeping the same type of reservation (package or room) - such as you have a package booked, and then are using a package discount. The same if you have a room only booked and then are using a room discount. If you have a room only booked and are switching to a package, then they will need to cancel everything and rebook and vice versa for package to room only.
Last year, I had a package booked and then the discounts came out - I used the Disney Visa package discount code and they applied that code to my existing reservation. They gave me new totals with the discount applied but everything else stayed the same - it was pretty easy!
To answer you other question, yes, you can have two reservations at one time - in 2011, we had reservations for 3 rooms through Disney and called to take advantage of an offer, this was before they could just apply the codes. At their suggestion, they booked us all new packages to make sure we got what we wanted before they cancelled our existing reservations.