This is possible. There is a VI call Set Default DAQ Configuration File that ships with NI-DAQ. You can find it in LabVIEW/vi.lib/daq/dqchnutl.llb. This VI will allow the user to programmatically select the configuration file. Some things to keep in mind are that you the device types and numbers must be the same between files. For example, if Device 1 is a PCI-6025E in one config file, the PCI-6025E must also be Device 1 in the other config file.