In order for WR to kick on when you need them, you need another implant connecting the WR to your adrenal gland. If you are going to bother doing that, might as well take the bioware that improves that too. You still have to deactivate them afterward. Now, I wouldn't charge essence for a small hookup like that, just extra nuyen, but that's me.
My policy is to activate the ware when a shadowrun begins, and turn it off when we are in a safehouse or in the clear.
I also think that you should work out with the GM a list of things you're character ALWAYS does. See, our characters are trained professionals that put their lives at risk every day. Most players are not. A character in that situation will be hyped up, their adrenaline surging and their sense hyper-keen. They are, essentially, paying a lot of attention. They won't forget things as much as a player does. Their lives depend on it. So, certain behaviors they display pre-mission become almost a ritual, and so happen every time. The GM can have a short list of things that are ALWAYS done, and make note of that. It isn't even that much extra work for the GM. It takes a minute to read the cheat sheet.