When splitting an Access database, you get a FrontEnd (FE) and a BackEnd (BE). What you would probably do is put a password on your BE like you did before. By default, your FE has the location of your BE, although if you change the location of your BE, you will have to use the Linked Table Manager in the FE to link to the new BE location. Once everything is in the right place and linked, you can simply rename your FE from ".accdb" to ".accdr".
When updating, your BE is usually going to stay the same since you don't want the data there to be replaced. Instead, you just have to replace the FE. As for the package manager, I haven't really used it in a while. I do recall that there was an annoying issue where if you choose to bundle the Runtime, it will fail to install the whole package if the Runtime is already installed on that computer. I think it may also not have removed the registries for the installation, so you get multiple entries when you go to Add/Remove Programs.
Of course, if you are deploying it and want to make sure no one can tinker with it, you will need to take some extra steps, such as turning off special keys, navigation panes, compiling the FE, etc.