Unicode-encoded Arabic fonts are ideal if multilingual font homogeneity is important, as they will almost always contain Western European characters as well as Arabic, all in the same design. In addition, most (but not all) Unicode-encoded Arabic fonts are available in the more modern OTF font format that will eventually replace the older TTF and PS font formats.
To check if a font is a properly Unicode-encoded Arabic font, you can open it in the Character Selection Dialog, and select the Arabic code page, where you should see Arabic characters.
You can also check that the Arabic characters are in the correct position by comparing the layout using your font to the layout obtained from using the Arial Unicode MS reference font.
Note that not all Arabic fonts will have all the officially defined ligatures of the Arabic language. The better fonts will have them all, or almost, but the cheaper, or free, ones may only have the most basic ligatures (such as lam-aleh).
Q++Studio will always select the most advanced ligature supported by the font used by each textual element. This means that, if some text is displayed using a basic Arabic font with only the most essential ligatures, then only these basic ligatures will be used. On the other hand, text displayed using a high-quality font with all the most complex, 2-3-4 letter ligatures, will be displayed taking full advantage of these advanced ligatures. If you change the font of some text in a QuarkXPress file, then if the new font does not support all the ligatures of the previous font, or if one font is AXT legacy and the other is Unicode-encoded, then you will need to re-process that Arabic text.