doing "hacks" the smart way?

[flat6]

I basically added some more functionality to things like the Admin CP and User CP. I didn't really go and touch the vB3 code too greatly - as a matter fact, I don't think I changed any of their functions. I merely added my own into their files when it was unavoidable (like adding buttons to Admin CP's index.php, that has to be "hacked" to get nav bar buttons) and whenever possible, I just made a new file, like added_admincp_functions.php.

Now, I have every intention of keeping my board up to date with vB's new releases. Is there any smart way to make my board readily upgradeable, outside of going through a change log manually? I think I may have heard of some tools that manage this merging automatically (ie. won't destroy my hacks) but I need more info on this.

So, basically, what's your strategy for keeping your board up to date while still lightly/smartly "hacking" it.