Welcome to the forum.
But as I’ve been looking at the specification of the speaker I see they have a power handling of 60W and the amp has a 100W output. Does this mean that the amp is too powerful for those speakers and they will be damaged? Or is power handling a minimum power requirement?
The Pioneer will not damage the speakers. Just be cautious when turning up the volume. If it seems like the speaker is distorting, turn it down. (It could be the speaker or the amp that is the cause of the distortion, but that is a whole other discussion.)
Also as I only have 3 speakers I will not be able to fill up all the channels on the amp. Is it ok to leave channels disconnected?
It is perfectly ok to use only 3 speakers. While we are on the subject of speakers, for your next purchase, go for a Subwoofer rather than the surround speakers. The JBLs will not do justice to the bass and low frequency effects. And, while we are on the subject of adding a subwoofer, use the Sub pre-out instead of the Subwoofer connection in the speaker terminals area.