[uawiki.org] Plug 'n Play drivers: Common Method/Via winnt.sif (method 1)
[uawiki.org] Plug 'n Play Drivers: Drivers From CD/DVD (method 2)

The Finishing method however (which will be renamed to 'Finisher Method' as of version 6.08, since there will be a new stand-alone program to handle it, called 'DriverPacks Finisher'), sets the method that will be used to execute the DriverPacks Finisher: this program handles all exceptions (mainly control panels, but it also fixes some drivers that would always get installed incorrectly), KTD and the cleanup.
GUIRunOnce executes just after the first logon, and so does RunOnceEx. The only difference is that RunOnceEx shows an installation progress. The option 'custom' allows you to set the execution of the DriverPacks Finisher manually. Here are some links with detailed explanations:

[uawiki.org] GUIRunOnce
[uawiki.org] RunOnceEx

And no, your own GUIRunOnce entries will NOT be overwritten. Nor will your RunOnceEx entries be overwritten.

I take it this is running the script to change the install paths so windows can automatically find drivers in the D folder?

Will this clear any other GUIRunOnce enteries?