when you're mounting the transducer on the transom. should you apply the silicone sealant before of after you put the screws for the mounting bracket in?

I put silicone in the hole and on the screws just in case. My boat always stays dry so I guess it worked.!!!

Gambler is correct.  Apply silicon to the holes and screws prior to mounting the transducer.  This way you assure you have silicon in all the right places.  You cannot accomplish this by applying silicon after mounting the transducer.

Remember, there are 2 types of silcone sealants - a rubberlike sealant  used around windows and doors, and another for use in an extremely wet environment. The latter's packaging states that it is for use above and below the waterline.  It's a polyurethane silicone sealer that is much better than the kind you find in most hardware stores.  It's more expensive, but is going to service you better.  Look for it in marinas or boat speciality catalogs.

how long does the sealant need to sit before i can put the boat in the water? i was thinking about installing it tomorrow but i don't want to disable my boat for the whole weekend seeing as i work and go to school all during the week.

You should not have to drill thru the transom, the mounting screws should not be that long. Make sure you read Glenn's post. Read the directions on the sealent you buy, it will tell you on how long to let it set up. Permatex makes some thats ready to go in an hour. Boat Life makes on that takes a week to set up but it is real good stuff. Going below the water line I would use it. Better to be safe than sorry.

The ones that take about a week are best.  My favorite is Sikaflex 292.  The stuff is incredible.

http://www.sikaindustry.com/ind/ipd-ma-products

I know this is not recommended but I was able to install my transducer with 3M Double sided tape.  This is the same tape used to put body pannels on most cars and Trucks.  

I chose this method because I could not determine the best location for my transducer and I wanted to test it before I started drilling holes.  The tape held so well I have left if on for three months.  And if I ever decide to remove it, you can cut the foam tape with some braided line in no time at all.

This may not work on a highspeed boat, but on my aluminum flatbottom and a 20 hp mercury it holds tight!

3m 5200 marine sealant/adhesive.  nuff said