I can try. ČEKAT is to wait and the verb is in imperfective grammatical aspect. It can take forever, it can be repeated. POČKAT is perfective. It happens once and when it is over, it is done. Sometimes this property makes a huge difference in meanings. In this case the line is little gray. You could use both and it would not really change the meaning.
I do think the lesson on aspect should be a bit sooner in the tree - maybe paired closer with the initial lessons on past tense? It's among the trickier ideas I've encountered in a language, and seems VERY important to Czech.
Wouldn't it work to use: 'Matej and Zofie were not waiting for us' as the continued form?
It wouldn't. Počkat is perfective; past continuous is progressive/imperfective.
Past continuous corresponds better to čekat: Matěj a Žofie na nás nečekali.