To illustrate how it can work, let's say you take Master Commando at level 40. That is good for a 10% increase to automatic rifle damage (Handmades, Fixers, combat rifles, assault rifles, SMGs, etc)
At level 41 you could take it again. Now you have the option to 'rank up' Master Commando. By combining the two cards you get +15% increase in damage (only first rank does 10%, each subsequent rank adds +5%) And at level 42 you can choose it again for another 5%. So in three levels you have increased your automatic rifle damage by +20%. The Master Commando card will now display a '3' on it and cannot be improved again.
You could also rank up the Commando card you already have, but that will add +5%, whereas the first rank of Master Commando will add 10%.
You have the option to choose three Commando perks. Commando, Expert Commando and Master Commando. If you rank up all of these you will increase your automatic rifle damage by +60% and it would use up nine of your allotted Perception points. The best return for a low investment would be to take the first rank of each Commando perk, adding +30% since the first rank of each is +10%. Then, as you level up you can rank these up, adding +5% with each one.
But this is limited since you can only have a maximum of 15 Perception points. If you look at the build I posted, you will see Expert Commando card is only at 2. Since I want to have other Perception perks besides Commando (like Concentrated Fire, Tank Killer and Fire in the Hole for example) I have to ensure they will all fit under the 15 point maximum, so my Commando only raises my auto rifle damage by +55% as a result. But I can live with the 5% lower figure since I can then run other perks in its place, like getting a throwing arc for my grenades.
To achieve anything in this game you must be prepared to dabble in the boundary of disaster — Stirling Moss