[theora] question on theora encoding

[Nikos Parastatidis]

Hello there,
I'm a university student and our professor assigned us as a project to 
build a theora encoder/decoder.
I need some help on some info that I didn't manage to find in Theora's 
reference.
I am building a function that calculates motion estimation. When making 
motion estimations must I scan each and every macroblock in coded order? 
After that the motion vectors should be stored in the same order? Except 
for that how should the program decide what kind of coding mode to use?

Thank you in advance
Nick