if I have an eclipse plugin/feature, which is released so that it has one p2 repository per each plugin version, that is present in eclipse marketplace, then will eclipse detect new versions of the plugin when I run check for updates? Or do I actually have to put all versions of the plugin in the same p2 repository, except those that are not compatible with some eclipse releases?
You have to put all versions of your plug-in into the same update site (p2 repository):
If a plug-in is installed via Eclipse Marketplace Client, the update site is added to Window > Preferences: Install/Update > Available Software Sites. Automatic update or Help > Check for Updates will search for updates in all available and enabled software/update sites.
Several p2 repositories can be combined to a composite repository.