I have a 99 sylvan pro select that has a small covering on the bow, which is where i need to mount the trolling motor. Immediately underneath that bow covering is a 3" or 4" wide metal brace that runs in the bow to stern direction. So it is impossible to drill through that cover without hitting the brace in a couple spots. Is it advisable to just drill through it? I cant think of another option. The pic shows a quick mount but I am not going to use it. 

I'm confused. Can you post a pic of what you are talking about? When you say bow to stern brace, those are generally not located where you are going to mount the trolling motor. That brace would be running low in the hull not high.