Yes, LabVIEW supports the use of MATLAB m-files using a MATLAB script node. For more information I would encourage you to post this question on the LabVIEW discussion forum, as there are a significant number of threads on that forum about interfacing with MATLAB. I have also attached a MATLAB/LabVIEW example from the NI website that may help.
As for the motion side, an onboard program would run independently of your MATLAB program running on the host computer, which may be beneficial to you if your MATLAB computations will require most of the PC resources.
For more information on onboard programming, please refer to the following tutorial:
Developer Zone Tut
orial: On-board Programming in FlexMotionBest wishes!
Dawna P.
Applications Engineer
National Instruments