What are your plans for the sand. Is the sand from a friends tank or is it dry sand or is it shipped to you. Moving over rock and water is really no big deal what so ever.
Step 1. Mix up about 10 gallons of top off water in a tub the day before you make the switch.
step 2. Go to a hardware store and get yourself a rigid plastic screen. Set this into your tank. This will help keep your rock off of the glass bottum and yett still be easily covered up by an inch of sand.
Step 3. Without stirring up you substrate move as much water as you can from the 29 over to the 45 tank. If you have to set corals on your substrate to get more water out then that is fine. Once your water is getting stirred up tand looking nasty then stop moving water over.
Step 4. Move you rock and corals and fish ( fish last ) into the new tank. Do not worry about aquascaping right now. You just want to get the rock into the new aquarium and under water.
Step 5. Once the make up water is the same temp and salinity as your tank water you can either pump it up into your tank with a powerhead and a hose or you can use a pitcher and add in the new water that way. Every half hour or so just add a couple pitchers of water or pump up a few gallons and in a few hours you will be done with the hard part. Do not fill the tank up all of the way until you are done aquascaping or you will be splashing water all oer the place. Now you can either Aquascape now or wait a couple days and do it then.
As far as the sand I don't know what type of sand you are getting. If it is dry sand then just slowly add in a couple cups or so each day until you have the desired depth. If you are really worried about an ammonia spike then get a tub and put the sand ( no more than an inch ) in with some salt water and a powerhead and test for ammonia in a few days. If you have ammonia then wait for the sand to cycle. If you have no ammonia then put that sand in and do somemore. If you get it from a store out of a tank then just have the store test the water. If it is the bagged stuff that is wet then just put it in your tank. You should not have and ammonia spikes and even if you do the live rock will take care of it before you can even test for it.
What you are doing is really not a big deal. You are just moving rock and fish from one tank to another and adding in sand.