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do warlock conceal powers affect the transport that the wraithguards are in? example, I get 5 wraithguards with 1 warlock with conceal and ride them in a wae serpent as per the wraithguard entry... does conceal confer that 5+ cover save to the serpent as well? According to conceal it works with the unit the warlock is with.... does the transport count? even if they are in it?

Well, since the word "with" is not defined as a rules-term by GW, the RAW is somewhat murky, but since a transported unit and the transport itself are always considered to be two separate units, I think you'll find very few players who think that the 5+ cover save would extend to the serpent.

For some back up on that, a squad inside a transport can use firing ports at a different squad than the transport can, i.e. 2 different units.

No.

Conceal only has an effect on the Warlock's unit (the wraithguard) as the transport can not get a warlock upgrade to benefit from it.