Silicone takes about a week to dry and needs to be dry to cure.
Aqueon makes black and clear sealant in smallish tubes I think 3 ounces and I found some clear in the big box store.
GE Silicone 1 Window and Door must be the #1 type because it doesn't have the mildew stuff which isn't aquarium safe.
You could lower the water level, and if there is any splash type areas you could use packing tape to tape on something plastic like trash bag or vinyl report covers to keep the water off of it. If you can smell the vinegar like smell from it it isn't cured. I haven't done this on my own tank with fish in it but I wouldn't be worried unless they were super delicate and super expensive fish.
Do the work on a nice warm day to allow good ventilation and the outer coat to dry quickly, maybe even a fan if you have one. To counteract the moisture of the tank evap.
Precautions should be taken to not allow and of the silicone globs to fall into the water.
My opinion is I would try it with the fish in. But you could always remove them to a plastic tote or 2. Catching them would be a pain though (and a bit stressful).
Maybe someone has actually done this, fish in tank to give actual experience.
Good luck with your project. Having water dripping out of the rim is not ideal.