Depends on the contract. Usually each allowance is a use it or lose it. We only had allowances for items we wanted to pick to customize, so flooring, countertops, cabinets and appliances.
Appliances we ended up asking for a credit off the purchase price and bought our own. We went through costco and got free install and a lot better warranty than anywhere else we looked. If you go this route make sure you bring up install as your builder may say you are responsible for getting them delivered and installed.
Another item I would suggest upgrading is garage door openers. I got the chamberlain ones that are wifi controllable, belt drive for quiet, much nicer than the cheap contractor grade they typically install. They said they wouldn't install but I could pay the door guys to do it and they gave me a credit for the included door opener.
Well then they installed their openers....so I had to uninstall those and install the ones I bought myself....that is after one of the ones they installed ripped out of the wall and ruined 2 panels of the door that took 2 months before they got it repainted. That is one example of the types of headaches you will deal with!
And I second what Hummer says about pictures. Take a ton! It will help later on if you have any issues, or want to see where studs are at for hanging something, or where wiring runs etc.