You can run several instances of MFPro, each with a different profile and set of triggers. The user manual will describe how to set up or copy a new profile. When you select a profile at the log in screen it will load the profile and the associated trigger file that was previously used with that profile.
If your trigger files operate on different markets then you can include them in the same trigger file, separated into blocks; eg. horse racing win markets, place markets, football over 2.5 etc.. This can be done by copying and pasting the blocks/triggers.