I'm going to answer this in parts.
if I had the ability contrary and I used acupressure would it have negative effects
If you have the ability Contrary and use Acupressure, you would lower a random stat.
would it have negative effects on my friend are if I used helping hand would it minus his attack
No, it wouldn't. Since Contrary only reverses stat changes on the Pokemon that has it, if it uses Helping Hand on another Pokemon it would still power up its next move.
if someone used shadow ball and it hit me with its extra ability (lowers sp def ) would I actually increase my sp def stat or is it more like every move I use that effects stats have a reverse outcome
If Shadow Balls secondary effect comes in, you would actually get your Sp. Def raised by the move. Pretty neat, huh?