When you get say, cybereyes rating 5, you get a capacity of 16 now if you load them up with addons that go beyond the .5 or lower Essence cost in cost of the add-ons does it add the to essence of the cybereye or does it not matter since you already have the essence lose due to the cybereye?

Any modifications that exceed the Capacity rating would take Essence instead.

to add on to what fortune said:

if your cybereyes have 16 capacity, you can choose to expend capacity instead of essence for the purposes of installing 'ware that goes into the cybereyes (and only the cybereyes). anything that does not have a capacity cost, or which has a capacity cost but is not eyeware, would still take up essence. once you have filled the 16 capacity of the cybereyes, any modifications beyond that which have a capacity cost can still be installed, it just costs essence instead of capacity.