You can fill up the coolant over flow to the full level, or slightly above or slightly below. The reference is just nice so that when you compare the engine cold a couple days from cold now, you will have a nice line to compare it to.
The main thing to get out of this that after you fill your rad to full, and have your coolant overflow to a known reference, a few days from now the rad should still be full, and the coolant overflow at the same level you left it at. If the rad is low, or the coolant over flow is drasticaly different (higher or lower) somethings funny....
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