There is a rule for problems like this:
When a character selects a class, he must choose to use the standard class features found in the Core Rulebook or those listed in one of the archetypes presented here.
You must chose a alternate class with your first level in that class. You cant add alternate classes later by RAW.
By RAW you can't do that, since you have to decide on your archetype when you take the first level in the class.
Your GM may or may not allow it, especially when it changes stuff you had for a long time and that you used a lot.
In my current campaign I have a level 10 plain old monk and I'm thinking of adding the Master of many styles at 11.
Now my question is do I lose all the things that are stated in the rules;
like at level 1 you would lose you monk bonus feat for one of the style feats, or do I keep it and just start as a new monk with the master of many style archetype?
You're supposed to pick it at the first level you take of that class.
In PFS, you can take an archetype at any time, as long as the archetype doesn't replace or modify an ability you already have.
In your case, it's basically a character rebuild, so it's not really any different than a ranger wanting to change combat styles, or a wizard changing his prohibited schools.
If your GM allows it, you'll need to rebuild your character from level 1, replacing/modifying everything that the archetype replaces or modifies. So whatever your bonus feats were will change to reflect the bonus feats from MoMS and you'll lose Flurry of blows to get Fuse Styles.