The purpose of this study is to compare the safety and effectiveness of saquinavir SGC plus stavudine (d4T) plus lamivudine (3TC) with that of saquinavir SGC plus nelfinavir plus d4T in patients with HIV-associated kidney disease. This study examines whether these drug combinations are effective in preventing kidney disease from progressing to a stage where it is immediately life threatening. This study also examines the effect these drug combinations have on the level of HIV detected in these patients. Finally, this study evaluates the drug level (the amount of drug found in the body) of these two combinations in patients with kidney disease.