I have separate tools for making my B&B products. I actually have three immersion blenders, one for FSG and lotions, one for CP soap and one for cooking. Each are different colors or models so I can tell which one is which.
As far as clean up goes, everything gets washed in the sink with hot soapy water and put away until I'm going to make a product. A few hours before I'm going to make something, I stick my tools in the dishwasher to get them as clean and sanitized as possible.