Right, these are codes that Stata uses for being more specific about what KIND of missing data you have. For our purposes (and yours, when you are cleaning data), I believe that referring to these with a simple period (.) will be sufficient, such as:
gen ValueIsMissing = 0
replace ValueIsMissing = 1 if Value ==.
this should do the same as
replace ValueIsMissing = 1 if Value==.a | Value==.c
(unless you have other kinds of missing values other than .a and .c)
Hope that is clear!