"Is there any way to avoid the matlab inbuilt functions?" Alternately use F11 and F10. I guess it's possible to write a conditional Step Into function, but I doubt it would be useful.
"break down [organize?] the code in a smart way and understand it easily" Isn't that what OOD is about. In that respect Matlab OOP doesn't differ much from other OO-languages. "I am new to Matlab OOP" but not to OO, since you added the tag, C++(?)