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This is doable (I've done it, actually) but risky. Uncured silicone is not safe for an aquarium and can poison the system. You need to be absolutely sure you don't drip any into the water while you're working, and you need to be sure it is fully cured before you refill the system.
Silicone cure times depends on the product. Read the label, and make sure you understand the bead size specified compared to what you're using. If it's claiming 48 hours for a 1/8" bead and you're using a 1/4" thick application, you may need 4 or 5 days.
The GE I and II products sold in home improvement stores will work fine, they're just not the absolute strongest - but for typical internal overflow box designs it's more than strong enough. Momentive RTV 108 is a silicone available through industrial supply (and amazon) that's stronger, if you want to be totally safe.
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Inconveniencing marine life since 1992
"It is my personal belief that reef aquaria should be thriving communities of biodiversity, representative of their wild counterparts, and not merely collections of pretty specimens growing on tidy clean rock shelves covered in purple coralline algae." (Eric Borneman)
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