The good news is: you're asking the right questions, and there are answers. The not-so-good news is it's a fair amount of work. There are 2 overall methods which you'll need:
1. Separation of Data method. This is an "interface file", with no real data; usually only one (or two) 1-record table, with constants and globals. It has almost all the business logic, scripts, layouts, etc.. It targets a "data file" with the data, calculations, etc.. Both have relationships, but the "data" file has minimal relationships.
The "interface" file can fairly easily be updated, without importing all the data. The "data" file, on the other hand, still would require the "import" you mentioned. But only when there are structural changes which you could not mirror (exactly) into a non-hosted production "data" file; you should stop the file(s) on FileMaker Server to make structural changes safely.
2. An "import/update" scripted routine to do as you say, import each table, into a Clone of the development "data" file. You are correct, updating the "next serial number" is critical. There are two methods to do so.
You will need to learn more about the above; there is information in several threads on this forum, and also at http://www.fmforums.com.
This is a good start: