After you've setup your repository, you'll want to make it useful for your users. What am I talking about??? Maintenance! You'll have to keep your files updated and you'll have to keep the indices updated.
An apt repository maintenance is very very very simple. You just update the packages in there and then regenerate the indices with the genpkglist command.
Tip: First test your new packages before making them publicly available; copy them to the specific directory where they belong to and then remove the old package. From now on, until you regenerate your pkglist file, you and your users won't be able to use this package. Upgrade the indices as soon as possible to get things back to work.
I was thinking but I don't really know what's better: copy everything to the directory they belong to, regenerate indices, remove the old packages, regenerate indices; or the copy, delete, (no file to download) regenerate indices approach (everything back to normal)... I thinks that's up to you and to how used is your apt repository.