It's really important that you the homeowner be fully involved everyday of construction, if possible, with the construction process. A home is a complex series of systems assembled by many different trades and even more different individuals.
Ask questions if you don't understand the process. Ask questions if you don't see your material selections being installed. Ask questions if you see what you feel is substandard work being done. The sooner a mistake is found the easier it is to fix or be changed.
The HVAC system is THE most important system and also the most complex because it uses electricity and plumbing in it's operation. It will impact your future enjoyment of the home everyday you live in it.
Your contract with the builder should detail the equipment used in your HVAC system.
that is how we rough in also as dan sw fl stated unless the furnace or air handler is not in attic. when the furnace or air handler is in garage or closet we install them at trim so they dont get stolen...