in need of help

Well i changed my valve cover gasket on the passenger side, put a new vaccum pump on, and replaced my fuel filter. I took my batteries out and had them charged. I found that i have red wire and black wire still unhooked and dont know where they go. I have a wire running to the alternator. Does one go to the vaccum pump? And i have a wire unplugged coming from the fuel filter. I know one goes under the fuel water seperator but idk where the other goes. I looked on ebay for a shop manual and found a 1993 but idk if it be the same on my 90. Can anyone help