Hi Piotr,
As you've seen, there are two ways to get MQX with KSDK right now with the 1.0.0 version.
1) KSDK Installation Package (MQX, FreeRTOS, uCOSII, uCOSIII)
Default Install Path: C:\Freescale\KSDK_1.0.0
Download from: http://freescale.com/ksdk
Includes KSDK+RTOSes Kernel
2) MQX for KSDK Installation Package (MQX only)
Default Install Path: C:\Freescale\MQX_KSDK_1.0.0
Download From: http://freescale.com/mqx/ksdk
Superset MQX package: Includes KSDK+MQX Kernel+RTCS+MFS
Both methods will get you all the features and files of KSDK. The only difference is the MQX for KSDK installation also includes the MQX MFS (Filesystem) and RTCS (Ethernet) stacks and does not include the FreeRTOS or uCOS kernels. MQX for KSDK is currently provided as a separate installer since it was released as Beta.
Also note that to get MQX when installing the normal "KSDK Installation Package", you must select the "Custom" installation and then on the next screen select MQX. After installation you'll see the MQX source at C:\Freescale\KSDK_1.0.0\rtos\mqx. If you do not see that folder, you'll need to re-install the KSDK package and make sure to select the "Custom" install.
When KSDK 1.1 is released in about a month, there will only be one installation package ("KSDK") and that should make it less confusing.
-Anthony