Can I ensure one son becomes vassal of another when I die?

You can't actually give your eldest son all the counties in the other duchy as of the 1.10 patch, so the situation you describe can't happen. Paradox wanted to close the exploit you mention for gavelkind, so now you are limited to giving your heir a single county. And if you gave your younger son the counties in the elder's ducal inheritance, the inheritance would simply change so that your unlanded eldest son inherited the other duchy instead: inheritance is always recalculated based on your current titles, not titles you once had.

The way to avoid the division of your realm on death is to eliminate one son's ducal inheritance. You can do that by giving him a bishopric (which makes him ineligible to inherit anything), by destroying a duchy title (thereby making one inherit the remaining duchy and the other only a county or two), or by having him conveniently expire before you do through various means.

Destroying the title is probably the "nicest" option, since you get to keep both sons alive and ruling. That would also keep your whole realm intact under a single duchy, and you can always recreate the title with a later ruler once you have the Kingdom or you have better succession laws.