I have read the "GoAnywhere MFT System Architecture Guide" but it does not address how internal transfers are handled by the cluster.
For example, if I have node1 and node2 MFT servers in a cluster, how do the internal users know which node to transfer the files to?
I'm assuming this can be done with a third part load balancer but I just want to get an idea of how others have handled this.

Thank you.

This is handled by the GACmd Client when calling GAMFT from the external Server (Java, C#, CLP, RPG, S4, Control M, etc...)

The API call has a "Server" parameter. You put both servers in the parameter and if it can't connect to the first, it connects to the second.

What if the user is using command line FTP from a windows command prompt? Or filezilla?

Then you will need to use an internal DNS, VIP or Load Balancer that points to the currently active server.

That's what I thought but I just wanted to make sure it was doable.
I plan on using a load balancer and round robin to each of the MFT servers.

We also have many users with auditor abilities on the MFT server.
If there are 2 nodes running the MFT then I'm assuming the https 8001 port can be used through an internal load balancer as well?

Yes, 8000 or 8001 will work the same way... only difference is SSL Security on 8001