How and when should I apply for M.Sc+B.Ed in different colleges?

Now, as per the government's the latest notice, you can pursue both the things together. But, I'll suggest you to continue only with B.Ed and then after that, go for M.Sc. M.Ed integrated course, as this would be more beneficial.

You can't apply for two degrees together. Only one will have value. Better do B.Ed first, then M.Sc.