What are you using to smooth it out?
I use a handy little tool that plugs onto the end of the tube, and ejects the silicone through a tiny hole right in front of a nice rounded smoothing edge. They are like $6 at the local hardware. You never have to worry about uneven silicone anywhere.
DEFINITELY remove all the old silicone. Use a razorblade to scrape ALL of it off the glass. Then wipe it down with rubbing alcohol. Mask the whole tank with painters tape before starting to re-silicone. That way you can peel away the tape after siliconing to have nice straight edges. That combined with a nice smoothing tool and you'll get good results.
Here is a link to the tool (in the middle) and the two other ones that are very helpfull.
http://www.homehardware.ca/en/rec/in...ppz/R-I2034700