Hopefully you have already converted to the APEX Tree implementation. This is important because the deprecated jsTree implementation will be removed in the next release of APEX so that we can update jQuery and Oracle JET libraries to the latest versions. Some people are still using the jsTree implementation because they have custom code to do things such as checkbox selection. Questions about how to do this and other things with the APEX Tree have come up many times on the APEX forums.
This article will describe how to add multiple selection with checkboxes to the APEX tree region. You can try it out here. You can also download the app. It is a 5.1.1 app but this technique should work in 5.0 as well.