Duplex have different zoning that may permit additional units.

If it helps, I've inserted a link to Cape Coral's permitting site below where you can check the status of work progress and inspections. 

You may could give them a license to use the land, provide a temporary or revocable easement or otherwise permit the use in some way.

NYC DOB considers a shelter a 'community facility with sleeping quarters' and may require a special permit for this use.Thanks Abel, You provided me with the right search terms to dig deeper. 

Applications were being lost, or the website wasn't permitting tenants to fill them out.

I think he calls it "pre-development" & goes over subdividing, entitlements, permits, etc.  

Does that mean I'm all set and can break it up in to separate units, or do I need to get a permit or rezone or other things?

This stuff will hit you if the things were done without permits..

The $56-a-unit process requires landlords to be up-to-date on their property taxes and for the properties to be free of any safety or building-code violations.Since landlords are not legally permitted to collect rent from tenants of a home with an inactive license, the system is designed to serve as a check on property owners, forcing them to address safety violations and pay their taxes.But Philadelphia’s Department of Licenses and Inspections lacks the resources to hunt down property owners who flout those rules, said Karen Guss, a spokesperson for the agency.

Another consideration is the permitting process and local zoning quirks, which can slow you down or force design changes mid-stream.