Transport Management System Configuration

Hi,
I have a question here, on Transport Management System.
We have new 64 bit boxes. I first migrated our dev SCM 4.0 box from 32 bit to 64 bit, it asked for being a Domain Controller. Configured it as a Domain Controller, and continued with the upgrade and completed the upgrade.
Now, I am going to the second box (QAS). I have performed the migration from 32 bit to 64 bit. Now, when I login to this box, in my understanding, TMS should offer to make this system part of the already existing domain right? It doesn't happen that way. It is forming itself again as a domain controller. After some changes and update configurations on both the boxes, the QAS box now says, "Waiting to be added into the domain by the domain controller" something similar to this. But, when I go and login to the domain controller (DEV), it doesn't show anything there.
In the QAS system when I go to the System Overview, I see both the systems but, they both show under the two different transport groups. I am totally confused here. Am I doing something wrong here? The only problem I see here is, the domain controller (DEV) is on SCM 5.0 as it is already upgraded from SCM 4.0 but the QAS is still in SCM 4.0 and waiting to be upgraded. Do you think this could be a potential problem? If so, what is the solution to continue with the upgrade because, I am sure the upgrade won't work without the Transport Management System configured properly.
Please help.
Thank you.

Hi Gus,
Thank you for the prompt response. Thank you.
There are couple of things to be considered before following your suggestion.
1. Our QAS box is in Kernel 6.40 (32 bit) and my DEV (upgraded) is in Kernel 7.00 (64 bit). In this kind of heterogeneous environment, I am sure the R3trans versions should be different. Is it possible to configure the transport management using the shared transport directory (Transport Group)?
2. Now, when I login to the QAS box, as I said in my previous message, I see two entries. One it should the APD (Domain Controller) with a different transport group. And I see the APQ in a different transport group. The problem here is, I cannot edit or delete any of the entries in the APQ - STMS because, it keeps saying all changes could be made only in the domain controller. A point to be noted here is, even though it shows two different transport group, it points to the same transport domain 'DOMAIN_APD'. Another thing to be noted here is when I look at the domain controller (APD), I don't see an entry for APQ or any awaiting approval requests.
Kindly suggest what needs to be done here.
Thank you.

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