Hey dear! I have one if you want to ask me any questions... I was confused at first too haha. You will have no problems leaving for an extended period of time, aside from "wasting" that chunk of the visa. As other have mentioned, the 6 months begins when it's stamped and the date it expires will remain the same and not be affected by any travel or extensions during that period. The only extension that will buy you more time is leaving and re-entering as close to the expiration date as possible, which will give you another 60 day stamp that you can extend for an extra 30 (to make it a "9 mo visa" so to speak). Getting an extension to remain in the country 90 day vs. 60 at any other point during the visa will not extend it, it just will be paying for the convenience of not doing a border run... I'm on budget and also much prefer a road trip to sitting at immigration all day, so I've been going to Mae Sai each time and making a little vacation of it, which has been cheap and lovely.
It seems like if you only want to stay for 2 or 3 months it might be more cost effective to get a single entry for 2 months and then extend if needed... then go wherever you're going and do that again when you want to return. The 6 mo could be great though if you're more interested in convenience and not having to worry about getting another visa when you return :)