Propagation and crossbreeding are two separate features
PROPAGATION (any planter type)
1. Put clone cut you want to propagate into farm storage box
2. Settings > Crop growing: turn on "Propagate clones?" and click the needed clone to select it for propagation
3. On needed planter, turn on "Use for propagating clones?"
Farmer will plant that clone in every free slot, cut new clones and put them into storage
CROSSBREEDING (large planter box only)
"Use for crossbreeding and cloning plants?" switch exists only on large planter box. Any other planter show only propagation switch, I think that's why it did not work for you
Settings > Crop growing: turn on "Crossbreed clones to achieve target genes?" or "Crossbreed clones based on the overall quality of their genes?"
Turn on the crossbreeding switch on EMPTY!!! large planter box
Put seeds or at least 2 different clones into farm storage
Farmer grows clones from seeds if needed (usually requires a lot of seeds), plants a center clone with neighbours around it, waits for it to grow, cuts the result and repeats until it matches your target. I recommend you to try on berry seeds first