I don't bother "cycling" suspension unless I'm building a long travel system. When I do, its to make sure I didn't miss something and have binding or rubbing due to miscalculation.
What your describing is called bottoming out. Your springs support the vehicle weight and your shocks control the speed the springs compress and expand.
If you change the weight of the vehicle, the tire rim weight/size, the springs have to change with them. The shocks match the springs.
Unfortunately, most lift kits are a "this spring fits all" and "this shock fits all" for a 2"- 4" lift. Based on how many people actually off-road their vehicle, this problem is frequently overlooked. Another issue is, most companies sell springs based on stock vehicle weight, only giving an option for hard or soft top.
Extending bump stops is done to keep the stock items from binding. If your vehicle had 3" of travel, you raised 2", you should have 5" of travel. Unfortunately now when the axle articulates, the angle is greater than it was stock and you have interferance or breakage. You move the Bump Stop up to prevent this and loose most of your travel. Now you bottom out.
So....onto your question. You have a few choices. Go with a stiffer spring and shock (this will effect ride), go slower off road (I cant seem to do this), run it the way it is and just watch what your doing. Remember the key point here, springs support weight. As you add weight, you should go to heavier spring. Match shock to this.
To set up a vehicle properly, it takes more than most places will do. They just order what's available and bolt it on not caring about anything other than just lifting the vehicle. My Landcruiser is lifted 2.5 inches. The springs and shocks are not even close to being correct. I'm waiting until I get done adding things on before I start getting serious about my suspension. I just deal with the bottoming out until then.
Scott