Advice? 46 gallon setup

Add an overflow and sump to get yourself more water volume. And add a better skimmer

 

There's some DC pumps I saw the other day that detect when water level is low and shut off so they won't burn out. Can't think of the brand I saw though.

 

I think most of the quality dc pumps have this feature. If they over rev or heat up they automatically go into a protect mode.

 

If it were mine I would drill the tank add a sump with a good skimmer and an algae scrubber and be good to go. Clean up crew I do some snails and hermit crabs and a diamond spot goby to sift the sand.
In my experience I like to use a refugium or an algae scrubber rather than reactors for medias. I have used them in the past but I like it a lot simpler now. And I float a small bag of carbon in my sump and change every 4 weeks.

 

I have a toms Rapids overflow box if you want. Is pretty safe it doesn't brake siphon if the power goes.

 

I use HOB overflows and have never had any issues with them. Nice option if you don't want to drill anything.

 

I'll second that on the HOB overflows. I've used them on many tanks for 10+ years and never had an overflow caused by one or loss of power. A well designed unit will not allow water to drain away from either end of the U tube so it won't loss its siphon.
I also agree that drilled is a great way to go but like in your case its not as easy with the tank up and running.