The most important task of any motion capture is to plan every step in advance. This is especially true for a large project.
If you use an optical system, just bring the data into Maya. You will need to make a virtual device to read in the motion. See MEL Command reference documentation for information on the defineVirtualDevice command.
We recommend using a single format for all of the motion you import into Maya. You can write a MEL script to define the virtual device that matches the data. With this method, you have to explicitly define the virtual device only once; other times you can run the script that calls the virtual device definition.
If no filtering is needed, try using the MEL movIn command. This does not require the construction of a virtual device.
To use all of the take management features and filters, you must define a virtual device and make attachments to it. Since most optical systems let you solve for joint angles, you can use forward kinematics. For a skeleton constructed with the same orientation as the solved optical skeleton, just attach the device to the rotations of the joints.
For a magnetic capture system, connecting the sensor axes to handles of RP of MC IK solvers works well.