If you are going to use manure as a fertilizer, then it's not a problem. Just mix with your regular fertilizers and apply like you would any other fertilizer.
Manure can be applied as a natural fungicide. It is one of the best natural fungicides. You can make a compost tea with manure by mixing 1 part manure to 5 parts water. Apply this tea to plants and weeds. It will prevent most fungus problems.