How will you begin to make changes in the Wordpress theme after which keep an eye on them for future them updates ?
You should use some kind of version control software like subversion to trace updates. Also when it comes to just "hacking", it's all located in PHP so that you can just drop to your theme making changes when needed to the files because they have to do with what for you to do. For instance to be able to make any kind of changes towards the header, typically you'd edit the header.php file.
One of the ways will be a version control system like Subversion.
My experience has proven that it is advisable to opt for a really well toned and easy to customize theme (from time to time compensated) that enables you to definitely make nearly all changes inside the theme's configurations instead of hard coding them. Once the theme is up-to-date through the author, whilst not impossible, I've found it's rare they have butchered something from the previous version. When they did, they'll frequently offer not just a reason but a potential work-around.
Another think is always to possess a testing atmosphere where one can check out new releases of the theme without jeopardizing injury to your live site. Just google 'wordpress testing environment' which should point you within the right direction. For that record, I run XAMPP on the spare home windows pc with this process.
Last little bit of advice: should you choose make any changes for your theme, back the theme files up regularly. In case something does go haywire, you won't be required to design the website on your own.