As zab so eloquently put :icon_tong , clearance is not really a requirement during training. For the Prop guys, we complete our ESPQ during Advanced training, right before winging. ESPQ is a very painful computer program that asks you a million questions, and you have to pretty much give a history of where you have been, what jobs, etc... That goes off and gets looked over. Based on that you will get an interim clearance. Depending on the paperwork, and your final clearance, you will get a follow on interview by NCIS. This is after they have looked your ESPQ paperwork over, and interviewed any previous bosses and friends/references you listed.
This is an ongoing thing, I believe your clearance is only good for 7 years, so save your ESPQ paperwork, or disk, so you don't have to start from zero all over again!