I'm going to assume that since you mentioned the Miskatonic Horror expansion and environments you're using the Act cards from that expansion and not the one originally present in King in Yellow.
For those that don't know the differences between the two: Originally in the King in Yellow expansion, the Acts only advanced when 'The Next Act Begins!' was drawn as a mythos card. The Miskatonic Horror expansion adds an alternative Act deck to use. This deck, in addition to advancing when 'The Next Act Begins' is drawn, advances when specific types of Environment Mythos Cards are drawn. Act I Begins when an Environment (Mystic) is drawn, Act II begins when an Environment (Urban) is drawn, and Act III begins when an Environment (Weather) is drawn. Another important difference between the two decks is the price that has to be paid to prevent an Act from beginning. In the original expansion, the price to prevent Act I and Act II from entering play was (respectively) by adding two doom tokens to the doom track and removing two elder sign tokens from the board. The MH version of the Act deck requires adding a single doom token and removing a single elder sign token from the board.
So, using the MH version or not makes a difference because the Act Cards are more likely to enter play, but the cost is less when they do.
Now, actually getting around to the question. For us, preventing an Act or not is a factor of how many expansions are in play, how many investigators are playing, who the Ancient One is, how far along the path to victory we are, and most importantly how lucky we're feeling.
First off, the large majority of the Act stopping we do is with Act I. Act II is really painful to stop. In a game where gate bursts already happen too often for comfort, choosing that voluntarily is just depressing.
With the original Act deck, the number of expansions is important. If we're using a lot of expansions, the odds of hitting a 'Next Act' card are pretty low since there's only ~7 of them, so we'll just let 'em pass. I don't know what the odds of of drawing specific types of weather cards, but I'll assume the chances are more or less the same regardless of how many expansions are in play, so when we're using the MH deck the expansion count doesn't really influence our decision.
The Ancient One you're up against is also important. You'll have to weigh a combination of doom track length, in-game effects, and difficulty of the final fight. If it's someone we think we can stomp in a fight, we'll stop Act I. Otherwise, if we're up against someone that wakes up quickly we'll let all of the Acts pass by. If they can eat us without blinking, since there's no chance for us later, we'll probably opt to stop Act II once. With Ancient Ones that have a longer track we'll look at what in-game effects they cause. We definitely won't stop Act II against AOs that make getting seals harder (Hastur, Yog).
If we're doing really well clue-token wise, or we have some Elder Signs to burn, or we've sealed some low-frequency locations, we'll feel pretty safe about stopping Act II. The penalty for removing seals is that the game goes on longer, but if you're fairly confident the additional mythos cards won't add doom tokens it may not be a bad choice. We'll have to be doing pretty well though if we're confident enough to get rid of a seal or two. We'll never stop Act II more than once.
TL;DR: Is the Ancient One going to eat you? Don't speed up the doom track! Don't remove a seal unless you're feeling pretty good! Do you have a shot at winning if it wakes up? Stop an Act once or twice! Find yourself thinking 'What are the odds'? Definitely stop an Act.
