In my case, I sent all my documents' soft copy to embassy first to ask if I am eligible for visa. They told me to send all papers including passport. I did through DHL (as it was from another country). The next day, they call me and asked me for the $40 deposit. One the deposit is done online, immediately they released my passport stamped with visa and a COE letter. For you case, I guess you visa and COE is approved alteady.
A company requires to show paid up capital 2 Million Thai Baht and at least 4 Thai staff for getting a Work Permit. However, best solution is to talk to a good business lawyer/accountant for the purpose. It's a bit complex, but not impossible to manage.