What can I do to manage my baby's intolerance for soy milk protein?

Read formula labels. You have to be very careful when choosing a formula as many "regular" formulas contain soy. Always discuss it with your doctor. Also if your baby is eating solids, avoid "hidden" sources of soy, such as miso and "hydrolized vegetable protein".
Allergy/intolerant? First you need to separate allergy from intolerance. Allergy testing by prick test (painless piece of plastic on back) will determine if it is allergy or intolerance. If you baby has a true allergy, then soy in any form can be a problem. To change the source of protein whether it is cow's milk based, elemental or other form, allergy testing can help determine what would be safe.
Use a nonsoy formula. 10% or more of babies allergic to milk formula are allergic to soy. If you are using soy formula for the above reason you may need to try a more elemental formula such as nutramigen or alimentum which do not have the major allergen in other milk based formulas.