When suing in small claims court, do I put the defendents physical address or the corporate address?

Well, that depends.  If the store is owned independently, you're probably going to want to serve the owners of the store (and that may be another corporate entity itself).  Go to sunbiz.org and search for the store under the fictitious name and then follow that info to the entity search.  Look for the "Registered Agent."  Then, you'll have ABC, Inc. d/b/a CDE, Corp. c/o Registered Agent at [address], and you serve that person/entity (the RA).  If the business isn't owned independently, use the same process, but you'll serve the registered agent for the corporate entity in Florida.  The corporatation doing business here should be registered as a foreign entity and then will be required to have a registered agent in the state of Florida.  If you serve the registered agent, you should be good to go.  I'd also say to check out the clerk of court in your county - generally there's some very helpful information regarding small claims.