Hello Mohamed,
PAL was introduced to HANA in a "only SQL way". That means that you first needed to create a PAL procedure via SQL. Later the concept of flowgraphs was introduced (for different aspects). Flowgraphs offers you the option to create the PAL procedure in a graphical way (e.g. supplying the parameter etc). But the outcome is the same: a PAL procedure. Shortly said: From a functional and result point of view regarding PAL there is not difference, flowgraphs just allows you to create the PAL procedure w/o SQL. The only difference is, that flowgraphs don't support all PAL functions, but this gap is continiuously closed (although each HANA SPS adds new PAL functions).
Regards,
Florian