This is a kind of tricky and at my opinion a hard thing to do.
What you need to do to close the stock is to line up the correct pikmin and to condition your opponent to certain attitudes at the battle.
As an example whenever they have 100% it's a good thing to make sure you have at least 1 blue with you, in order to seek that 150% (average) to secure the upthrow kill.
But that's not the only way to take a stock, you can gimp, catch a roll, fall with nair to dsmash, etc.
As far as I know, Olimar doesn't have true kill combos to rely on that, because they are dependent to the enemy, but it does have some setups. It's important to note the pikmin you will use to take the stock too.
Purple will often take stocks more easily with any move due to knockback and so on with their properties.
If you are still having troubles closing the stock, try to not focusing on taking the stock, instead of that try to keep stacking damage and sooner than later it will finish it without you being aware. At high % you might want to stop throwing pikmins because they don't latch too much and don't do heavy damage, except for the white of course.
It's a tricky thing because when you gather all the condition to get the kill and you just focus on getting the stock by a certain way, an experienced player may notice that and you will tend to repeat more movements than before, leaving a spot to your enemy to punish that behavior.