These are a couple of funny words, if English is your second language they may be confusing to you. Both of them are basically slang/contractions of "what do you." They aren't officially words.
Whatcha = "what do you"
Whatchoo = "what do you", used only for rhetorical questions...the difference is that the "choo" sound comes from emphasizing the "you" part, which you would only do in a rhetorical question. For example,
"whatchoo lookin' at?" meaning, "stop looking at that"
or "whatchoo know about math?" meaning "you obviously don't know anything about math"
That's all