let's consider the verb "kuha" (take / get):
'KumUHA KA ng pagkain." ('get a food')
"KUHAin MO ang pagkain." ('get the food')
the verb "kita" (see):
"nakaKITA KA na ng multo?" ('have you seen a ghost?')
"naKITA MO ba yung multo?" ('did you see the ghost?')
"ka" is I believe, a short term of the pronoun "ikaw" (you) which gives an emphasis to the subject while "mo" gives more emphasis to the object. although, if you happen to be a native tagalog speaker, you won't be able to observe their differences except on the form of the 'tagalog verb' being used.
here's the trick,
when using "mo", the main verb's affix is placed at the beggining and mostly at the end of the word while "ka", either at the beginning or at the middle of the word.
'talon' (jump)
"tUMalon ka!" (you jump!)
"talonIN mo!" (jump on/from it!)
'kain' (eat)
'kUMain ka." (eat/have some.)
"kainIN mo." (eat it.)
'takbo' (run)
"tUMakbo ka!" (run!)
"takboHIN mo!" (run for it!)
:)