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I am in the middle of a game with my Black Templars against a Grey Knight Inquisition army, I assaulted a group of guardsmen, and 2 sentinels. My crusader Squad raped the guardsmen as expected, However there were unresolved wounds from my Emp's Champion.

Do the unresolved wounds get rerolled against the Sentinels to see if they damage them?

or are they just wasted wounds?

You must declare where you are allocating your attacks before you strike blows,meaning what models are attacking what unit. If you strike blows with one unit and they are wiped the wounds do not transfer to the other.

As above. See allocating attacks. Excess wounds against a unit are lost.