One thing these Clintons did was to place these political appointees into civil service positions which are not positions that President Bush could vacate without cause. I also believe that the Clintons war room never ended just was transitioned from the White House to a Senate space.
What specific positions are you referring to? Do you have any examples?
The leaking McCarthy was one such conversion and per post #149, a great link by Freeper Jane Austin gives positions converted, although names are not named.