Today is Monday but our school decided to use wednesdays timetable

For each day in the substitution software you can manually change the day (week/term). This timetable day is then used to determine what has to be substituted.

Use menu Settings/Day in timetable, then use the arrows at the bottom of the dialog:

Every time you change the day(week or term) the program asks if the following days should also be shifted.

In online substitution, you can change day/week/term in similar way.