It can cover the entire die, either side of the IHS (cover) and any copper or nickel heatsink/block. do not under any circumstance use CLU on any aluminum surface. Do not get it on the line of capacitors next to the die. Cover those with a nonconductive TIM such as MX-4 or liquid electrical tape.
CLU is not difficult to spread, but don't expect it to be anything like normal TIM. It will require more work than yours probably going to be expecting. Its slow to spread, but not difficult. Use as little as possible and just keep working the brush. You'll be amazed how far such a small amount will spread. Completely cover the top of the die. Do a die-sized spread on the underside of the IHS as well, not the entire underside. Again use as little as possible. You're basically painting a thin layer on, and don't want it squeezing out to the sides of the die because its just going to be wasted and further risks contact with the capacitors, although this shouldn't be a concern as you should have already covered them.
Its very straightforward and will greatly help with temperatures. Just be patient. Since you have the IHS removed and have already voided your warranty, now would be the time to lap the top of the IHS if you were consideing it. Just take a photo of the information on top of the IHS beforehand, or keep the original packaging for chip details in case you ever wish to sell it.