Yes the buses run about every thirty minutes - even in the green season. be aware that they don't run after about 9.00 PM.
The bus fare is under 300 colones which is less than 60 cents (can't remember the exact amount as it rose slightly in December.) You do not need exact change - the drivers are used to giving you change. But I really wouldn't try to give them anything much bigger than a 2000 colones bill.
On the road between Quepos and MA, there are a lot more stops than those indicated on the Cupo Tico map. As a rule they are every several hundred metres. Much of the location depends on there being a safe area for the bus to pull over as the road is narrow and hilly and winding. Once you are there you will figure out where they are - some are easily recognizable, others not so. Ask someone where you are staying where the closest one is or if you go somewhere - the same and they will point you...
Re taxis, although there is supposed to be a law in CR that all cabs are supposed to use their metres (called la maria) - in MA most never do and get away with it. Therefore, yes, it is best to ask the price before you get in and have some sort of an idea what a fair price is to your destination. Most normal rides for places not far off the main road will be somewhere between 2000 and 4000 colones.
Stick to the official licenced red taxis - not the pirates.
If you are charged a flat rate - you really don't need to tip as basically they have already built it in - unless of course you think you want to give the driver a bit extra.