Id say no to the silcone on the bulkheads, you will one day want to replace or change something and will be stuck as they are siliconed in.
Yes a 2nd overflow pipe is good, it saves alot of work cleaning up, and replacing equiptment and livestock, let alone the carpeting.
The last question i think is a matter of opnion here you can go either way, i have always siliconed mine in, is yours glass or acrylic, if acryic you may want to try the rubber seal if that hold better, as silcone and acrylic do not bond very well.
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