It's possible that you either misunderstood the process or were just given bad information.
When you apply for the license, you need to specify the frequency or frequencies you want. From what it sounds like you want to do, you'll require the assistance of a frequency coordinator to find suitable and available frequencies.
Unless you are applying for a itinerant frequency, the FCC will require a frequency coordinator to sign off on this.
Once you have the frequency pair licensed, you can build out the repeater system.
If you are just beginning this process, you might want to talk to a local radio shop first. Here's why:
1. They can assist with the licensing. They can also help you contact a frequency coordinator.
2. They can help you decide what sort of system you need. Depending on what type of business you are running, what your coverage needs are, what your budget is, etc. they can help.
Consider that it may be easier/cheaper to just rent radio service from one of the local shops. While having your own repeater might seem like an easy solution, it often isn't. Repeaters can be expensive, several thousand for a decent one. Add in the duplexer, coaxial cable, antenna(s), tower site, etc. and you can easily spend $10,000 to $20,000 or more on a decent repeater. The site will be important, too. For the repeater to work well and have good coverage, you are going to need a tall building, tall tower, or access to a mountain top site for the system. That means you either need to have access to this or pay someone for it. Usually tower space leasing can be on the order for several hundred dollars a month or more.
Renting radio air time from a shop can be a whole lot cheaper, plus you can benefit from much wider area coverage.
If putting up your own repeater is really the direction you want to go, you really need to talk to a competent radio shop. Putting up your own repeater is not easy. It requires some very expensive test equipment to make it all work correctly. The skills, tools and experience necessary are important, and this is where the shop can really help out.