After you have done all your changes with nLite and only creating the ISO remains.
All your changes are complete - only then - run DriverPacks BASE add the driverpacks and create the ISO.
Make no changes to your files after DriverPacks... If you make changes after DriverPacks you will create problems.

This is outlined in great detail in the tutorial... This also covered in every forum at DriverPacks.net

I admit the tutorial is a little old... but every thing there is still valid.
Some of the newer features have not been documented yet
but you don't need them for what you wish to do.

I would create a copy of the source folder after you are done making your changes.
Then add DriverPacks to the copy of the source.
in this way if you need to make changes you can fall back to the pre DriverPacks source and make a new copy
Make your changes to the copy
add DriverPacks last
create ISO.
  - DriverPacks can be uninstalled from DriverPacks BASE (select no packs and hit slipstream) but the above method is better still.

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I have a dollar that says your queston (any driverpacks related question) has already been answered somewhere here at the DriverPacks.net forum.

Oh, also, how to I add specific drivers needed for my system?