nonomiya,
An embedded PXI controller runs ETS.  You can consider the RT Series plug-in boards the same as well.  From the point of view of LabVIEW Real-Time using those two as Real-Time targets, you don't need to distinguish the two.  They both will be targetted pretty similarly.  The difference is that the RT Series plug-in boards don't have a local hard-drive, as mentioned in my previous post.
You are correct that no matter which Real-Time target, you will need to develop your VI in LabVIEW Real-Time and then deploy them to the Real-Time target.
If you have a Real-Time system set up, you will need to find the appropriate driver for your Real-Time system and determine if the driver supports the DAQ device.  The NI-DAQmx and Traditional NI-DAQ drivers support the S Series, E Series, and B Series DAQ devices.  NI-DAQmx supports the M Seris devices.  As discussed in 
this KnowledgeBase I mentioned in my previous post, ETS suports NI-DAQmx and Traditional NI-DAQ.  The Traditional NI-DAQ driver is a legacy driver, so if possible, I would choose a DAQ device that is supported in NI-DAQmx.  Another thing I should mention is that USB DAQ devices are not recommended as USB as a bus is not deterministic by nature.  The SCC Series devices are signal conditioning devices, so I wouldn't group them in with the M, S, E, and B Series DAQ devices, but you can use our Signal conditioning modules in a Real-Time system.  R Series devices are used for data acquisition, but they actually utilize an FPGA, so they need the NI-RIO driver.
For a RTX system, only the NI-DAQmx Base driver is supported, as mentioned in the KB I referenced in the last paragraph.  This eliminates some options for DAQ drivers, so an ETS system is a more flexible choice as far as devices go.  If you need help with hardware recommendations, I would recommend that you contact your local National Instruments Sales Engineer, as they can help suggest products that will best fit your application.  Thanks!
Thaison V
Applications Engineer
National Instruments