Keep in mind that I, myself, am still learning. From looking at the kanji that you are working on, from what you have said, there aren’t a lot of good examples. Numbers are a bit of an oddity from what I’ve seen. They usually use the on’yomi readings when by themselves, which is different from most other kanji that I’ve learned.
I’m currently working on section 8-2, and the pattern that most of them follow, is that if it is one kanji by itself, it will use the kun’yomi reading. For example, if you see 人 by itself, it is most likely ひと.
If you see a kanji with hiragana attached, then it will also most likely use the kun’yomi reading. For example, numbers used as counters that you have learned. 九つ for “9 things”, since it has the つ attached, it is most likely ここのつ.
If you see two kanji attached to each other with no hiragana, you will usually use the on’yomi readings. There are no kanji that you have studied that follow this rule yet though. The first good one comes in the next section (3-1) so I will try to give an example from that one, and you can see it when you get to it (sorry!).
The kanji 口 is a perfect example of all of the rules. 口 by itself uses the kun’yomi reading. 入り口 is two kanji with hiragana attached and uses the kun’yomi readings again. 人口 is two kanji together with no hiragana and uses the on’yomi readings for both.

Sorry for the long-winded reply, but hopefully it helps a little. :)

Hey Joel, do you happen to have the Anki link for Radicals7? I couldn’t find it in the lessons.

Ah fair enough. Thanks for clearing it up. :)