Regardless of what Miss Francis, your typing teacher, said in 8th grade, we do not need to have control over everything in life. Learning to live sometimes means letting go, and that includes letting go of your Camera Connection Kit caps.
Sure, those caps are spiffy and fit your connectors just so, but in real life use, you don't really need them. You can safely dispose of them for recycling after unpacking your connectors. In my case, I find it much harder to remember where my connectors are than to worry about non-functional end caps.
What I do is this: I have a specific home for my connectors. I bought a small pencil box from Staples, and when my connectors are not attached to my iPad, I always put them back into the pencil box, along with my VGA cable. This box lives on my shelf in the iPhone/iPod/iPad accessories area. If you feel you must keep track of your caps, you may want to have a specific place for them to live (like my pencil box) when they're not attached to your connectors.
Love right backatcha,