Should I use the Arabic Presentation Forms provided in Unicode?

Quick Answer

No. These forms were provided to provide round-trip conversions to legacy encodings, but you should ignore these and use the characters in the main Arabic block for your content.

Doing so means that your content can be understood better by applications, especially when it comes to searching and similar operations.

[I think there are actually one or two characters embedded in the presentation area that are for normal use, but i can't remember what they are at the moment.]

Details

The Unicode Standard contains two blocks of presentation forms for Arabic, Arabic Presentation Forms-A, and Arabic Presentation Forms-B. The characters in these blocks are contextually-determined joining forms, such as U+FB75 ARABIC LETTER DYEH MEDIAL FORM and U+FC76 ARABIC LIGATURE THEH WITH REH FINAL FORM.