To save you the time spent disassembling your suspension twice, I'd wait until you had the Koni Yellows in your hands
before installing your springs. That way, you only have to take the car apart once, and once you've completed the install, you can be done with it for good. The Koni shocks are very well built, and will easily last 150,000 miles. Furthermore, the Konis are designed to work with lowering springs, while your stock shocks are not. In fact, you could wind up damaging other suspension parts by running your stock shocks at such a low height.
If you're concerned about getting an alarm, then I'd focus on that first. After all, if the car were to be stolen [god forbid], the rest of it becomes irrelevant.
h:
So my advice again is to enjoy the car with the stock springs and shocks for the next month or so. Then, once you have the parts ready to do the job properly, install the aftermarket springs and shocks together in one shot.
