To do the job right, the widows should be removed, and, the butyl replaced. The windows are "squeezed" on the walls, trim ring on the inside is drawn tight, squeezing the butyl that is on the inside edge of the outside part of the window.
To seal with silicone only on the outside may, or, may not get the job done.
To be sure, it is a two person job to do it right, but, doing what you had done, is way better than nothing, and, yes, it is ok to not seal the bottom...hope it all works out...
Back to a 5'er after 4 yrs fulltime.
Pulling with a '14 2500 ram, 6.4 Hemi.
Montana High Country 31RE