Here's the simplest way i can put it i think, lets say your on PLD, well as a PLD you have to sometimes pick weather you want to be main tank or off-tank, so the skill Iron Will you'd want to put on a filter, so that lets say when the filter is enabled Iron Will will activate and when the filter is disabled the skill will deactivate.
Best way to set that up in minion is to add the "Iron Will" skill to a profile twice, and set up the extra filter #1 for it.
The first "Iron Will" in the skill editor we'll use to turn the ability on, so in the skill editor under the basic section will set filter #1 to enabled (which will cause it to only use this skill if filter 1 is on), and under player buffs we'll check for the missing buff ID of 79 which is the buff you get when Iron Will is active (so if filter 1 is on and the player is missing buff 79 this skill will be used).
For the second "Iron Will" in the skill editor you'll want to set the filter 1 to disabled (so the skill will only go off when the filter is disabled), and under player buffs we'll check if the player already has buff ID 79, so this second "Iron Will" will only be used to turn off "Iron Will" and the first one will only be used to turn on "Iron Will"
It's not something that complicated that a flowchart is needed hopefully this information i've given you today is enough for you to understand the concept of how filters work in minion.
Also it's not just limited to turning one skill ON and OFF, but lets say you're a healer and you make a profile with good DPS however sometimes in endgame dungeons you need to focus a bit more on heals then DPS, what you can do is put all the DPS moves on one filter so that when that filter is ON only then will the healer profile DPS. Another good example would be to put "area of effect" moves on a filter so that you can choose weather you want your toon to single target DPS or DPS everything around you. Another good one it's used on alot is controlling the usage of Buffs for when you want to manually use them at certain times yourself.
Best way to set that up in minion is to add the "Iron Will" skill to a profile twice, and set up the extra filter #1 for it.
The first "Iron Will" in the skill editor we'll use to turn the ability on, so in the skill editor under the basic section will set filter #1 to enabled (which will cause it to only use this skill if filter 1 is on), and under player buffs we'll check for the missing buff ID of 79 which is the buff you get when Iron Will is active (so if filter 1 is on and the player is missing buff 79 this skill will be used).
For the second "Iron Will" in the skill editor you'll want to set the filter 1 to disabled (so the skill will only go off when the filter is disabled), and under player buffs we'll check if the player already has buff ID 79, so this second "Iron Will" will only be used to turn off "Iron Will" and the first one will only be used to turn on "Iron Will"
It's not something that complicated that a flowchart is needed hopefully this information i've given you today is enough for you to understand the concept of how filters work in minion.
Also it's not just limited to turning one skill ON and OFF, but lets say you're a healer and you make a profile with good DPS however sometimes in endgame dungeons you need to focus a bit more on heals then DPS, what you can do is put all the DPS moves on one filter so that when that filter is ON only then will the healer profile DPS. Another good example would be to put "area of effect" moves on a filter so that you can choose weather you want your toon to single target DPS or DPS everything around you. Another good one it's used on alot is controlling the usage of Buffs for when you want to manually use them at certain times yourself.