I have read the Enemies negative Quality out of the Runner Companion. The way it read in the book (My Interpretation) is that you take the Connection + The Enemy Rating (Anti Loyalty) and Multiply it by the Threshold however the answer may not show up in multiples of five...am I reading this correct.

? It looks to me like you add the (modified)Connection + Incident Rating, with an Enemy Group being a modifier to the Connection as per p.124.

The hard cap to all Enemies added together should not exceed 25 BPs.

Each enemy raises your Notoriety by +1 as well.

Edit: If you mean the actual test, a GM rolls the Incidence Rating (1-6) of each enemy before a scenario, and compares it to the Incidence Thresholds Table to determine the result.

If You add (modified)Connection + Incident Rating You can have any variable between 2 and 12...The positive and negative Qualities in all books are staged by 5's. If I have an enemy of 2 (1 for Connection and 1 for Incident) is that a 2 point negative quality or is that a 5 point negative quality

Qualities do not have to be staged by fives, though you're correct that this protocol is generally followed. If you have an enemy of 2, it's a 2 point negative quality.