You should say "there were a lot of glasses ...."
You can say the one at the bottom, the one in the middle, the one on the top or the big one on the top, the red one at the bottom.
Regarding the second question, some possible alternatives are listed below:
"Could you kindly help me with this question?"
" Could you let me know what the answer to this question is?"
"Could you please help me with it?"
" I wonder if you can help me with this question?"