...as I may have mentioned, I was unaware of this when I designed the character. It wasn't so much an issue for adepts on previous versions (3rd being the last one I regularly played under). From several sources where I have inquired about this, all mention that the background count is subtracted from the final initiative roll (eg. 3d6 + 11 - 2) That is good.
From what I heard and read this is sort of how I understand things now though a few questions remain.
fFor powers, that directly affect dice pools of any skill test, it will be negatively affected by the count's rating. So for example, for an adept in Chicago, unless she has a power with multiple rating levels that is greater than 2, the power will effectively be negated and only the base dice in the pools will apply to the test. For example, an adept using Improved ability 2 will only have their normal dice pool for the test (as if they didn't have the power). Now the one question I have is, if the background count exceeds the power's rating, is the base dice pool further adjusted by the increased count? Same for a power like Attribute Boost - Agility 2, the adept will only get the dice for her magic attribute, without the power as her pool. If the count increases to 3, does she subtract another die from the test (and so on the worse it gets)? Another area that still seems a bit hazy are powers like Enhanced Accuracy, linguist, or Sustenance which do have any affect on a dice pool, would these be negatively affected as well and how would that be handled?
For foci it seems pretty straightforward, if the background count is equal to greater than the force, they simply will not activate.
This really should have been spelled out a little better in the rules as it is no small consequence for awakened characters, particularly adepts. I've spent nearly two days asking around on various forums and looking for any detailed and definitive description.