As you say, s represents spot beams that deliver locals to different cities. C means CONtinental US. Many of the s transponders will be low or zero signal because they are not pointing at you, so you can ignore them when aligning the dish.
99 and 103 represent the location of the satellite along the equator.
A and B represent the frequency band (A or B-band).
Just to confuse you, these are not necessarily satellites as such, they are groups of transponders. So two spotbeam transponders at 103s can actually be on different satellites.
When you are aligning the dish, you always get alignment on 101 first. Apart from spotbeams on 101, the 101 transponders should all be in the high 90s or even 100. 99 and 103 should be pretty well aligned automatically. Fine tuning should get most 99ca/cb/103ca/cb transponders into the high 80s at least, preferably mid 90s.