protusions in assembly mode

Of course you can. You can either create an Assembly Feature (a feature that only appears in the Assembly itself, not in the Part files comprising the Assembly) or you can Convert or Offset sketches or edges from a Part in an Assembly to another Part while editing that part in Assembly Mode. See Help on "top-down design".

'Sporky'

um, i think you can only add a cut(s) in an assy.

Ack -- you're right. I was thinking about Welds . . . but those are also Parts.