I have a character with Bio worth 3 points of essense and Cyber ware worth 2 point of essense. The character also has Sensitive System. Is total essense loss:

Bio > Cyber
Cyber = 2 * 50% * 2 = 2
Bio = 3
Total = 3 + 2 = 5

or
Bio < Cyber * 2
Cyber = 2 * 2 = 4
Bio = 3 * 50% = 1.5
Total = 4 + 1.5 = 5.5

As far as i can see in all cases it would be favorable to double essense after rather than before. However i don't see where it gives the exact order of the calculations/comparisons. The comparison though does seem to be made on the essense assigned to the 'ware, so i personally see the former as being the case. Thoughts?

P.S. I don't see this as being an issue often. Typically if you have the Sensitive System flaw you are going to be rather light on Cyberware, if you have any at all.

Before.
Qualities should be determined prior to assigning BP to Nuyen.

Your second example is correct. You determine the final Essence costs of the Cyberware and Bioware before you determine which one is halved.