You can use either MeanAnomaly or MeanLongitude in EllipticalOrbit to specify where the spacecraft was in its orbit relative to the perilune (i.e. relative to where it was closest to the Moon) on Jan. 1, 2000. By default, if they aren't specified, they have a value of 0.0 on Jan. 1, 2000; i.e. the spacecraft was at perilune on January 1st, 2000.
Alternatively, you can specify the Epoch when your orbital elements were correct -- i.e. the actual date when the spacecraft was at perilune.
SSC parameters are described at http://en.wikibooks.org/wiki/Celestia/SSC_File