Clomid & Cysts

Good Afternoon Ladies,

I will try to keep this brief but to make a long story short I have irregular cycles (AF rarely shows up on her own and I can go a year or so without her ever showing up). DH and I have been TTC for a year now and as of last month my gyno started me on 50 mg of Clomid only to find out that I never O'd. So my doc decided to put me on 100 mg starting this month. I then went in on Friday for an u/s (which was my CD 11) & found out that I have a TON of cysts on my ovaries. He couldn't believe how many cysts I had. I told him that my mom also developed cysts on her ovaries with every fertility drug she took and so unfort this comes to no surprise for me However I still have hope that medicine has come a long way from when my mom was ttc. Either way, I still cried and was very upset that this cycle is a bust but I am coming to grips with it. He mentioned the possibility of me seeing an RE (since right now I see a gyno, however the office also deals with infertility), but he was thinking that he would start me on Femara. With the u/s on Friday he also told me for sure that I have PCOS and that he needs to research Femara more before he will prescribe it to me. Therefore, he is having me come back on Feb. 3rd to sit down with him and discuss starting me on Femara as well as for him to perscribe Provera to induce AF.

 Therefore, My numerous questions to you ladies are as follows:

What are the main differences between Clomid & Femara. I know Clomid thins out your lining and femara doesn't (or isn't supposed to) but does it help with PCOS women, more than clomid? I have only just begun researching this option and was wondering what you all thought.

If I see an RE, is that considered fertility since I only have a certain amount of fertility costs covered by my insurance?  

How long does it take to get rid of cysts on your ovaries and what do you do since I am sure they won't all go away on their home? These are all qustions I thought of after leaving the office (that is when my mind actually started to think besides crying) otherwise I would have asked the doc myself.

TIA.