About your first question:
There a lot of factors that can influence the choice of the signaling protocol; however because your phone are al at one site i think h323 could be a good choice.
(keep in mind if you use h323 you must do the most of your work on te GW while using MGCP is easier)
About your second question(if you use h323)
You have to perform on the GW a dialpeer voice 'tag' pots with destination pattern the DNs you want your analog phones have
and a dialpeer voice 'tag1' voip with the appropriate destination-pattern and pointing
to your CCM.
On the CCM site configure a route pattern pointing to your GW in order ip phone can call analog phone attacched to the FXS ports
hope this help