This is a guide on how to set up SourceSplit to work well for categories that require beating the game multiple times (e.g. All Main Categories and All Achievements). The main issue is that when using a regular SourceSplit setup, the timer will reset whenever you go back to 00.

Option 1 (allows for Auto Start and Stop): Use 2838's fork of SourceSplit, which most importantly for this use case has seperate options for Auto Start/End/Reset, where regular SourceSplit has these combined. Also this version basically just expands on regular SourceSplit, so with the right set of settings this can function the same as regular SourceSplit. The specific settings you need of course depend on how your splits are set up, but the one thing you definitely wanna do is turn off Auto Reset. This way the timer won't reset in 00. Auto Start will still start at the very first 00, and Auto End will split whenever GLaDOS dies. To install this version of SourceSplit, just download the LiveSplit.SourceSplit.dll from the Releases page HERE, and replace the original LiveSplit.SourceSplit.dll in your Livesplit\Components folder (you probably want to back up the original one somewhere though). The autosplitter and the settings should then be available in the Edit Splits menu just like regular SourceSplit. So in summary, you (most likely) want the following settings: Auto Split - Disabled, Auto Start - Enabled, Auto End - Enabled, Auto Reset - Disabled.

Option 2: If you don't wanna do the above, you can just use regular SourceSplit and disable Auto Start/End/Reset, however this means you'll have to manually start and stop, aswell as split between runs. Since that is gonna be slightly inaccurate you'll have to go through the video afterwards and check the timer at the exact start and stop points in order to retime.