Confused...Number of Entries? Length of Stay? Valid until? China vs. Hong Kong- What do I need?

Confused! I am going to do research at a university for 12 weeks near Hongzhou. I would like to site see during research period with weekend trips to Tianjin, Shanghai, Xian and Hong Kong, and after project is finished go to Beijing. Looking at roughly 100 days in China. I have been told by Application Center that I need a BUSINESS-F and they will give double entry for 90 days. If I have a double entry that is for 90 days, can I go to Hong Kong part way thru my research, for a weekend (say after 60 days) and re-enter mainland after the weekend? Would my 90 days start over again when I re-enter from HongKong, thus allowing me to site see beyond my 12 week research project(ie. another 90 days on top of the 60 I already will have spent there)? I am worried that a 90 day F will expire before I do all the touring I want to do there if I don't exit to Hong Kong(I will be busy with research for 87 of those days). I would like to spend 7-10 days in Beijing after my research finishes, but a 90 day F only gives me 2-3 days after my research is done. What does the Valid until part mean...that I have to enter before that date? Valid until does not mean I have to exit by that date does it? What is my entry date....the date I leave Canada to fly, or the date I land in China? Please help me sort this out!