For slow cooker meal prep should I freeze the vegetables separately from the meat and sauce?
If you're doing a one step cook in the slow cooker, you can freeze everything together. If you want to brown any ingredients first you'll need to keep them separate. I do tend to, so I'd have a bag for any meat, a bag for veg that wants browning or softening (onions, carrots, pepperd etc.) and a bag or other container for the liquid part, with any veg that doesn't need an initial step (beans, sweetcorn, potatoes...) 

Most slow cooked dishes freeze very well after cooking, so an alternative is to cook several portions at once, divide and freeze, microwaving when you want to eat them. These approaches aren't mutually exclusive of course.