Hi @Sam_Joel,
That’s a good question. My company (OpenCraft) has dealt with this a lot and we recommend that you avoid forking the Open edX platform if at all possible, for exactly that reason - the more you customize your fork, the harder it is to maintain, and the more work is required for applying security patches or upgrading to the new release.
Instead, try to build your customizations using the platform’s many extension points. If you read through that document carefully, you’ll see that a huge range of customizations is possible without actually forking the platform. And if you want to do something that’s not currently possible with the existing extension points, I encourage you to create a new extension point to make it possible, and then contribute that extension point to the platform so that everyone can benefit and you can avoid having to maintain a fork.
If you want more specific guidance, please give us an idea of what sort of customizations you have in mind.