Advice needed: How does Plesk affect manual upgrades and vice-versa

[adaw]

We just purchased a dedicated server with Plesk installed.

As Plesk is unfamiliar territory here, we are wondering how it interacts with Apache, etc. For example, I understand that it manages all the updates to Apache?

What happens if we need to recompile apache with some custom modules? Or recompile PHP with a custom library?

i.e. What happens if we do any manual upgrades ourselves? How will that affect Plesk?

Would appreciate any advice you have.

Thank you