To my eyes, the fact that you have 9 different websites/stores running off the install is of minor importance. You will encounter the same issues that any dev / live Magento set-up will encounter. At the point the site launches you will need to create a second copy of your database / code for use as a development environment. With regards to the code, I would hope that you are using some kind of VCS such as Git or SVN, if you aren't you should seriously consider it.
The database is the slightly trickier side of things. It is also going to be the issue exacerbated by the fact you have 9 different websites, since you will have a lot of different configurations. There will likely be 3 different types of configuration changes to be made.
1.) A setting that needs changing for the live websites.
2.) A setting that needs changing for a future website to be launched.
3.) A setting that needs changing in order to make your development site work.
The 3rd type is the easiest to deal with. You can simply change them in the database and forget about them. These will include things like setting the base_url values in core_config_data.
The 2nd type should ideally be made with migrations rather than through the UI. If you are using Source Control these migrations would be kept in a branch that will get merged into your master branch at the point you wish to launch the website they effect (at the point the code is merged, you may have to do some tinkering with the version numbers based on how you deal with type 1.
The 1st type can be handled in one of two ways, a migration is a favourable option as it means all installs of you code dev / staging / live can be kept in sync. If needs be, simply ensuring you update your dev database at the same time as the live one, would suffice.
Some of the things you need to change won't necessarily be the easiest things to achieve through migrations, but doing so should prevent any errors from arising whereby you forget to update a single value on one of your servers.