Entering multiple voices on the same staff
Many people will want just to write a single melody on the staff, but sometimes you need additional harmony notes or even additional polyphonic voices. Each staff can carry as many as 8 separate melodic tracks or voices, though it would be rare to find music with more than 4 parts per staff.
The basic principle in multipart writing is that one of the voices defines the time of each measure - one voice's notes and rests must take up the entire value of the measure. We call that voice the primary track or "track one." Additional tracks can then be freely added without any requirement that their time fill the whole measure (this is the typical case, though in strict polyphonic writing it's musically desirable to make each voice complete in itself).
To add additional tracks to an existing passage just choose the desired note values, as you did before, and click in the music where you want them to go.
It's best to think as you do this about consistency of voices. If you're adding a second track, for example, it will generally work better musically if the notes of that track are not too far apart in pitch; it's good to let the notes of each track seem to follow each other naturally.
If you enter a note or rest into a secondary track, or click on one that's already entered in a secondary track you'll notice that symbols in all the other tracks will turn green. Only the symbols of the currently active track will be black, and only those will be selectable by dragging a selection rectangle or by using the "Select All" command. This allows you to tell at a glance which notes are in which tracks, and also makes it easier to select specific tracks. When you're in track one, though, all notes, rests, and other symbols will appear in black and when in track one you can select all tracks at once.
Notice above that when you have more than one track in a staff it will have more than one handle at its left. The outermost handle is for track one, and the currently chosen track is in red.
Short cuts
If you are entering notes by step entry (choosing rhythmic values and then playing the notes on the keyboard) Practica Musica will enter on the same stem any notes that are played at the same time (or even approximately the same time). So if your multiple parts are very simple you can enter them just by playing the notes:
When entering notes either directly in the staff or via the keyboard, the number keys provide a good shortcut for changing note or rest values.