Take a look at the Hardware Guide of the Edison Module . The UART2 is the one for the control terminal for Linux. You can use the UART1 as an alternative for an extra UART, this one is connected to the pins: 46,63,61 and 54 (J17 - pin 14 / J18 - pin 12 / J18 - pin 13 / J19 - pin 8). In this way you could use the OTG port, the Serial Terminal (with cable) and a UART connected to those pins.
In order to change the functionality of the ports, using the OTG to interact to the Serial Console you could try this: Galileo Getting Started Guide - learn.sparkfun.com (That one is for Galileo but it will give you an idea on how to do it in Edison) You should know that using this method, the interactions are very slow and I recommend to use the ports with their default functions.
I'm not sure if it's possible to change the functionality of the USB-B port but you could try with something like the sketch or remapping the ports while you create a new image.
Take a look at the description of the different port in the board: Using Serialx on Edison
What I ended up doing is cutting apart a USB-RS-232 cable and a OTG cable and splicing them together. I then mounted the DB-9 connector directly to the box. The advantage of this is that the USB-RS-232 cable has the line drivers so the savings from having the UART is really minimal. Splicing the cables saved the space and I got the line drivers. The cables cost $14 and I would have spent that on level converters so I am satisfied. I also have found another product that has 2 or 4 RS-232 outputs from a single USB cable so that is another possibility for next time. For now I have already built the second UART driver so my problem is solved for these first two boxes. The next ones will likely use the other solution.