Use the "Add PC" form to add a player character and the "Add Enemy" form to add an opponent. They are not mechanically different, apart from coloring.
You don't have to add the characters taking part in combat at initiative order - when adding a combatant he will be automatically placed at the correct position. However, be warned that if you add a new combatant after the combat sequence has started, the initiative order will be sorted again.
When adding effects, you need to specify which character(s) it affects by filling in the name that you've given them using the "Add PC" or "Add Enemy" form. If it influences more than one combatant, you need to apply the effect one combatant at a time (meaning, you can't provide a coma-separated list of names). In the 'Effect' field you just provide a name to distinguish between events. Duration is the number of rounds that the effect lasts for; should the bar reach zero, the effect is automatically removed from all affected combatants.
The upper right button toggles the effects information for each combatant.
The bottom right button finished the current combatant's turn, puts him at the end of the list. Additionally, it reduces the duration of the effects, if a round has been completed since their initiation.
I'm planning to add hit point tracking with adjustments (for damage and healing)