Their are numerous posts up here on how to hook up/connect a Flex 6700 to the SPE 2K FA. I wanted to summarize and make clear several points.
First, the USB port on the SPE 2K FA is for computer to amp communication only. You may not use this to hook the Flex 6700 up directly to the amp.
Hooking the amp via the RS 232 portion of the DB 15 connectors provided by SPE, then to a USB to serial adapter that plugs into the USB port of the Flex is the only way to do it.
You only need three lines RX, TX and GND to have CAT communication between the devices.
ALC does not work properly. It is actually very quick and easy to program the power out of the Flex per band to the Amp. Very quick. I left the default values except where they needed to be increased or decreased to have things right.
Auto on DOES WORK. VDC are low but seems to get the job done. So, when you turn on your Flex radio, the amp comes on too. I have the "quiet" Fan mode enabled so unless I'm transmitting its silent. Very nice.
PTT via the DB 15 works just fine.
You must be feeding a very well tuned antenna for this stuff to make any sense at all and that load needs to be stable or else each time you operate your going to have to adjust the input power to the amp from the Flex. In other words, make sure either your antennas are tuned properly over the range of frequencies you intend to work, or, that your antenna tuner automatic or otherwise, always provides the same load/swr.
What if you want to use the second SCU? Well, no problem. Once again, have Dan make you up a second cable. Ignore the accessory hook up for the second amp and just use the RS 232 to USB as noted above. The RS232 will hang out of Dan's cable. In the same way you hooked the first one up to a USB to serial adapter which plugged into the 6700 so you'll do that again here. Have the ANT 2 hooked into the second input. Define a USB/CAT setup for the second USB hook up so that band data from the second slice will be sent over. I'd recommend using the choice of "follow the RECEIVER" so that the second slice will always have port two of the amp set up when you pull the TX over there. Others may have different ideas and you'll choose what works best for you.
You can have your cables made by Dan Tassll his contact info is on the SPE Expert web home page at the bottom. He's highly responsive. On weekends he's frequently at shows with his wife and will only respond by email late at night. But he will get back to you and on the following Monday your cable will likely be on its way. Just order it in advance of your amp arriving and when the amp arrives its about as plug and play as it gets.