Lowering the car with stock shocks/struts cause serious handling problems. I saw a video of a Civic that was lowered really far on stock shocks, and when he was on the highway he started to drift into the left lane a little... well he jerked the car back to the right slightly to get back in his lane. The dampning and spring rates were so messed up because of the stock shocks that the rear end bounced around, he slid backwards across two lanes of traffic and went over the cement median strip. Looks like he destroyed his rims, tires, body kit, exhaust, suspension parts, and whatever else was under his car at the time.

Just do your shocks at the same time as the springs/coilovers. Be safe.