If they are asking for originals of something and you don't have them because you sent them for your PR, you write a cover letter saying that and include copies. If you don't have enough space on the application itself to convince them she will leave again after her work permit expires if the two of you don't get PR, then write an extra letter. Sometimes people are refused because they don't believe they will go back. They may have given you a temporary permit based on you having strong ties to your home country and will not overstay because you are leaving your wife behind but if your wife joins you, what are her ties and who is she leaving behind? It depends on the embassy in your home country. Some embassies seem to believe that everybody will overstay but you never know if you don't try.