I'm still a little confused, but let me try to address some things:

When you say "The main account is actually my domain account, which is coupled to Gmail," what does that mean? Does that mean it's a Google Apps account? Or are you just set up on your web host to forward emails to a domain you own to a GMail account? For example, you own archeon.com, and have set up [email protected] to forward to [email protected]. You may never use [email protected], instead sending and receiving from GMail as [email protected] and just using GMail for mail handling. Naturally, the best way to do such a thing would be to pay $50 a year for Google Apps and truly integrate your domain with GMail through MX and SRV records, but then it isn't free.

Am I close on this part?

The other part is about using GMail account A to check GMail accounts B and C through POP. Naturally, this will work, but probably isn't ideal. Regardless, it would be helpful to know how this part is set up in order to fix your issue. When GMail account A checks B and C, are you telling it to leave a copy when it retrieves the mail?

If I were in your situation, I would log into all three accounts in my browser separately and then switch between them in one tab, or open one tab for each inbox. That would keep the accounts separate.

On Android, I think you want to handle things very differently than you are now. First, K447's suggestion would be the one I'd jump to immediately. From the description of your setup, it sounds like account A is already getting emails from B and C, but you've also set up your phone to get emails directly from accounts B and C. If those connections are POP, then it makes sense that your read status isn't synced because that's impossible with POP.

But this still leaves me confused, because it sounds like you should be seeing double emails on your phone. Account A would get emails from accounts B and C, and accounts B and C are pulling email to the phone separately.