For Glyph Substitutions you must add OpenType features, which FontCreator doesn’t currently support. You can, of course, create all of the required medial forms in FontCreator.
You can add GSUB tables using the free tool from Microsoft VOLT or the freeware program linked to in this thread — Adding OpenType Features
Ligatures can also use GSUB features, or they can be mapped for manual insertion as we do for ff, fi, fl, ffi, ffl ligatures in Latin scripts. Several Arabic Presentation Forms are defined in CompositeData.xml which is used by the Complete Composites feature in FontCreator