First of all, may I draw your attention on the terms you're using? You probably mean Open Type fonts instead of Open fonts. Open Type is a type of font like Type 1, True Type, etc.
This said, the big point of Open Type fonts is the amazingly wide range of possible glyphs. I invite you to read Adobe's page about that font format: http://www.adobe.com/type/opentype/. It's very interesting.
Such a format thus allows designer to gather I would say all their glyphs in a single font rather than having a font, its Expert set, etc. Plus it supports special functions as alternative glyphs in a given environment and many more.
Now you're saying you're on version 6.5 of Quark and that's the problem for you. At that time, Quark would not support OT fonts nor Unicode. It means you can use those fonts but you are stuck to the 256 first glyphs and have no access to OT functions. If you replace OT fonts with their equivalent Type 1, you'll probably get mismatch. So if you're working with Type 1 fonts, you must go on with Expert set along in order to access special ligatures. If you are working with OT fonts, you won't be able to access extended range of glyphs in v6. Is this clear?