What does it mean when some creatures put two +1/+1 counters onto another creature? Does that mean a) target 3/3 creature becomes 5/5 or b) the creature is now 1/1 + 1/1 + 3/3 and the enemy has to first destroy this creature with 1/1, when the creature dies, the next enemy has to destroy the second 1/1 on this creature and next, the enemy has to destroy the creature with 3/3? For example, card Scrounging Bandar. And does putting a -1/-1 counter on that creature means a 3/3 creature becomes 2/2? And does putting a +1/+1 counter on target creature mean the same thing, like putting a +1/+1 on target creature?
It means option A but there's slightly more to it. +1/+1 and -1/-1 counters alter the creature's power and toughness and stay on the creature unless some effect removes them. Compare putting 3 +1/+1 counters on something to Giant Growth, an instant which reads
Target creature gets +3/+3 until end of turn
If both are targeting a 1/1; each one will result in a 4/4, however Giant Growth will wear off at the end step making the creature a 1/1 again whereas the counters will keep the creature as a 4/4.
-1/-1 Counters work the same way, each one will shrink a creature's power and toughness, to the point where if they have 0 toughness, they'll die due to state-based actions.
Final thing to note is that +1/+1 counters negate -1/-1 counters and vice-versa at a 1:1 rate. For example, if Baleful Ammit which reads
when Baleful Ammit, enters the battlefield put a -1/-1 counter on target creature you control.
targeted a 2/2 creature that had two +1/+1 counters on it, the -1/-1 and one +1/+1 counter would be removed (also due to SBA) resulting in the creature now being a 3/3 (a 2/2 with one +1/+1 counter on it)