At this point, the GPS receivers are connected to your PC through the USB port and are ready to configure and verify that all is working OK.
Ublox provides a nice evaluation software package for Windows called u-center that makes this very easy. You can download it for free from here. It makes it easy to explore all the configuration options for your receivers and make sure everything is working properly before we move to RTKLIB.
After you have downloaded the program and started it up, use the "Port" option in the "Receiver" tab to select one of the USB ports that the receivers are connected to. They will probably be the only two options. In my case they are "COM3" and "COM4".
[Update 11/27/16: If you don't see your receivers listed in the Port menu it is probably related to some recent windows driver changes from COM ports to location sensors. See this post for details]
You should see the connection status box at the bottom of the window go to green and list the baud rate that the receiver is configured for, probably 9600 baud if you haven't changed it. If everything is working properly, you should now be able to click on the various display icons and see sky positions, signal strengths, status, etc for all the satellites the receiver is tracking.
To configure the receiver, select the "Configuration View" from the View menu. All of the receiver configuration options for this receiver will appear in the menu and you can read what the currently is set to with the "Poll" button or change the configuration by changing the settings and hitting "Send". For details on what all these settings mean, see the Neo-M8 Receiver Description.
I recommend first increasing the baud rate to something faster than the 9600 default. I found 115200 worked fine with my setup as long as I don't have too many extra messages enabled, 230400 should be fine for almost any settings. To do this, select "PRT" from the "Configure" window and set the "Baudrate" field to 115200, then select the "Send" button at the bottom of the page. You may need to re-select the port to let the eval software match its baudrate to the receiver.
Next, select the "Messages View" from the "View" tab. From here, you can see which NMEA messages are enabled and being output by the receiver. The enabled messages are displayed in bold. You may want to disable all of them to reduce unnecessary information from being continuously transferred over the serial port. We will be using Ublox specific binary messages for RTKLIB so do not need any of the NMEA messages enabled. Be aware, though, that the eval software is using these messages, so if you disable them, the display windows will stop updating. To enable or disable a message, right click on it and select the appropriate action.
Once you have the receiver configured properly, you will want to save the settings to the on-board flash. Do this from the "CFG" menu item on the "Configuration View" by selecting "Save current configuration" and then the "Send" button.
We still need to enable the raw receiver outputs for pseudorange and carrier phase, but since they require using unsupported commands, we will do that from RTKLIB.
Now do the same for the second receiver.