A module with an install file gets run at install, for an example if you install/enable a module with one `hook_install` and three `hook_update_` all of those will be ran, and the database will be set to the last `hook_update_` so if you where to add a new `hook_update_` you could run update.php which would run that hook function.

The best way to do what you want to do is create a module like you want, with a empty `hook_install` then just keep adding `hook_update_` functions as you need to do more stuff, then when you are done run update.php to run all the hooks.

It may also be a good idea to separate the types of stuff you want to do into groups (like create new items, and add them to the database, then another hook could be delete x and y, and another could be rename a and b) and add them as `hook_update_` so for example if you need to run something more then once for an example or maybe down the road, you could just call update.php and run that specific `hook_update_` function (if you for example wanted to run delete x and y more then once, you can).