Any ideas for installing baffles to an existing setup?

It is designed to fit into the existing sump chamber (having it custom made out of Acrylic). The existing chamber's flow goes under the stock baffle, but a refugium's outflow should always flow over the top of a baffle. So instead of re-engineering my sump and adding a baffle while the tank is live, I am just having an insert built to the inside dimensions of my sump chamber, but an inch shorter (right to left) so that the water will enter the insert from my tank's overflow, fill-up the insert, then flow over the shorter (top to bottom) side. I'll send a pic when it comes in.
 
fyi silicon will cure under water. You still need to hold the structure still in place for that to take place properly
 
Is the insert going to wedge into place or what? This is an interesting idea as well. Especially since you can block off the light from reaching into places you don't want it.
Sorry, I should have clarified that the insert is a topless box with one of the sides, where the water flows out, being shorter than the other 3 sides.
 

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