You should need -pack option:
-pack option can be used to group the set of compiled objects under the single module name.
You can do
ocaml -p -o src1.cmo src1/a.cmo src1/b.cmo
ocaml -p -o src2.cmo src2/a.cmo src2/b.cmo
In you file, you will need call Src1.A.xxx or Src2.B.xxx ...
Notes, it is better to avoid similarily named files in source tree :)