I'll start this by saying I am no expert.
I am not sure what you said answers the question.
If you take a well designed system and add a duct here and add a duct there.... the velocity in the ducts start getting slower and slower. As the velocity drops below an acceptable level the collection falls off and dust can settle on the bottom of the duct and then you start to have all kinds of problems.
If you close too many ducts you reduce velocity and the ability if the collector to work.
So limiting factors are fan capacity (ability to breath in) and filter capacity (ability to breath out).
If your bags do not breath the system will not be able to hit its design capacity. Dust bag/filters do not last forever. They need to be replaced at some point. Do you have a magnehelic gage on the collector? I believe it tells the pressure differential from one side of the filters to the other. When it gets too high and cleaning will no longer make it come down it is time to replace the filters.
From your velocity comment it sounds like you got someone in to look at your system? In past systems I have found when we start to add things, eliminate things, close ducts it becomes a mess. If I was in your situation the first things I would do is make sure what I have is designed correctly.
Take a drawing of your machinery needs (duct size) and location and give it to a competent designer and see what they say. You might further define what is "on" all day and what is very intermittent. They may be able to fix the problem with a good design and some automatic gates of some type. Eco gate is an automatic gate system and a fan control system. There are other more basic systems that use an electro-pneumatic valve that triggers the gate using voltage from the starter control circuit.
I put a link to a company I use to design systems and they sell gates. They happen to be local to me so I am very lucky.
On that page they have the most basic automatic gates. Call for a quote, the listed prices I have found are not what you pay.
If you have totally outgrown your system, the filters/bags are good you come to the one system or two question but I would do the research first its "free".