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I know that the matrix of leadership was something good and the other one was something to do with the decepticons. Were they really good or evil?

other one?

other one?

There's also:
Mini-con Matrix: http://tfwiki.net/wiki/Mini-Con_Matrix
Matrix of Purification: http://tfwiki.net/wiki/Matrix_of_Purification
Matrix of Conquest: http://tfwiki.net/wiki/Matrix_of_Conquest
Dead Matrix: http://tfwiki.net/wiki/Dead_Matrix

I think the Dead Matrix is the best known of the ones I listed.

I could be mistaken, and probably am, but I think most of the TF continuities, with the exception of G1 (and maybe others), have a pair of good/evil matrices.

Don't forget the

Matrix of Wronski-fication
and the
OTHER Dead Matrix!