Need to do some more extensive modifications than just css… how? Possible without losing everythin

I need to do some more “heavy” modifications to some of the pages, and it would be far better to make some changes to the php/html than just hiding elements with css, is there any way I can do this without losing the changes on next update?

Example: In Event Calendar Pro (or “the event calendar” at the wordpress repository for the free version) you can make a “events” folder in your theme, copy a file from the plugin and make any kind of changes to it, and the plugin will then automatically use the file in your “events” folder instead.