MIDI Files

The following MIDI file formats are supported:

.MID files: Standard MIDI files. Additionally, .MIDI and .KAR files can be imported, pasted or dropped, they'll be renamed to .MID automatically.
.MIDI2 files: MIDI 2.0 Clip Files. This is a recent format that can store MIDI 2.0 features. It isn't widely supported yet.
.MPT files: MIDI Pattern Track files (see MIDI Pattern Editing).

.MID files can be saved as .MPT files and vice versa.

A MIDI file can contain more than one stream (called a "track" in MIDI terminology, but renamed here to avoid confusion). MultitrackStudio supports using multiple streams in a track, although this is not recommended.

MultitrackStudio does not support patch changes within a stream. If a program change or bank change is encountered while opening a file, a new stream will be created. Furthermore, MultitrackStudio streams can only send messages to one MIDI channel (using the channel the program change was sent to). So if a stream in your file sends messages to more than one MIDI channel (which is bad practice anyway), the file may not load as intended.

MIDI 2.0

.midi2 files can't be opened directly in a track. If you import one, it will be converted to a .mid file. The MIDI 2.0 information is retained (see below). Exporting to .midi2 is available in the MIDI Export window and in track editors.

Under the hood
MultitrackStudio stores MIDI 2.0 per-note controls in MIDI 1.0 files as NRPN values. Any software other than MultitrackStudio won't recognize the per-note control values in exported MIDI files, but it will still load the files.
The higher MIDI 2.0 resolutions (16 bits for velocity, 32 bits for controllers, etc.) are preserved in .mid files used in tracks as well, again using NRPN parameters. The high resolutions do not appear in exported .MID files, unlike per-note controls.