Since you have a lot of questions here I'll try to go through in list form for efficiency:

What about the other side effects like the anemia, Luekemia (sic), Low blood Marrow etc.

These are the affects that occur in humans and in cats -- and are not usually seen in dogs except with very long-term therapy (several months, usually). If any of these effects are seen, they will resolve with stopping the drug.

He will be on it for 30 days, 250mg/8h=750 mg/ day. Is your opinion still the same about it.

Yes, I believe that is an appropriate dose protocol (for a dog weighing approximately 10-12 pounds), and I've used that approach successfully in dozens of dogs previously, with good efficacy and safety.

furthermore. I believe he has has it before when he was on Baytril and Ciprofloxacin (not sure of the spelling) will this treatment limit its recurrence if he resumes the Flagyl regimen.

MRSA is not typically carried on dogs, it's likely he picked it up from a human who was carrying it, possibly without any symptoms. It is important to continue treatment to the point of a negative follow-up culture.

I'm not sure what you're referring to about resuming Flagyl, that's not a drug that has any real use in managing skin problems.

And if I have to wear glove to handle it why would I want it in his system.

He's a dog, you're a human. Protecting yourself from more common side effects is important -- his body is far less likely to experience side effects.

I have used calendula tincute (sic) on it and it kills it but it does pop up elsewhere. Also, what about colonization. . .what does that mean?

Colonization is simply the process of bacteria multiplying and spreading across a surface, be it skin, or other organs, or a tabletop, etc.