Amps won't burn up anything, it's the volts that will burn fuses if there is more than 14-15 volts.
Voltage is simply a measurement of electrical potential or force, similar to water pressure in a water line. Voltage alone doesn't do anything, it is the current (or actual flow of electrons) that does the damage when a circuit (path for the electrons to flow) is completed. 200 volts won't do anything if there is no current flow. As far as the original question, yes you can install the alternator now and add your accessories later.