The sequencer is where the occurance of events on the timeline is controlled. It's the part you can make visible or hide by dragging the thin horizontal bar right above the transport panel. When playing a song, what Reason actually does is run through the sequencer from left to right, and doing everything the sequencer tells it to do. So on the sequencer, actions are specified like "play a C3 note with this device", "switch from pattern A1 to A2 on that device" etc.

There are two views for the sequencer: Arrange mode, which is standard selected, provides a global overview on the structure and elements of your song.

Horizontally, the sequencer is divided in multiple sequencer tracks. Every sequencer track corresponds to a device on the rack, and contains the actions Reason should do for that device. Typically, for a matrix it contains the pattern changes that happen during the song. The sequencer track of a device can contain different elements that represent the sort of "information" it contains: a yellow horizontal bar is for pattern changes, a blue horizontal bar is for recorded slider/knob movements, and little red vertical stripes represent individual notes.

The most useful thing you can do in Arrange View is to group elements of your song that belong together so they can be easily dragged, copied and pasted. This you do by selecting the pencil tool and then dragging it over the part of the sequencer track you want to group. Try it, and then make it a habit to do this all the time! The coloured blocks you create like this can be cut, copied and pasted with the usual Ctrl+X, Ctrl+C and Ctrl+V.