You need to give each board a unique serial number.
For the LAUNCHXL2-RM57L we set all serial numbers the same so that they consistently give the same UART COM port # in windows when you plug in different boards.
But you can change this by using the XDSDFU utility:
c:\ti\ccsv7\ccs_base\common\uscif\xds110\xdsdfu.exe
the -s option sets the serial number.
Try the -e option first, the serial number format is something like HL57R00 if memory serves me so you could make it '01' for your second board, etc.
There are some generic instructions here: 
That also talk about how to change the serial number.
When they have different serial numbers, windows will give them different COM ports so your UART issue will be taken care of.
Then in CCS you have to change the .CCXML file to connect to a specific board serial number, so you will make one CCXML file for each board.
The CCXML file can be opened in CCS. There is a Target Configuration screen, with tabs.
The tabs are 'Basic', 'Advanced' and 'Source'.
Go to the 'Advanced' tab, and highlight 'Texas Instruments XDS110 USB Debug Probe' in the connection tree on the left side of the window. You'll see 'Connection Properties' in the right side. There is an option 'Debug Probe Selection' it defaults to 'Only one XDS110 installed'. If you change that to the other option - which is 'Select by serial number' then you will get another box where you can enter the serial number as reported by XDSDFU.
This will make that CCXML always connect to the board with that particular serial number.
In this way - you can have unique CCXML,LaunchPad pairs and use them to connect to specific launchpads.
