It doesn't matter. Merging is essentially a fusion of the two units.
The only things that you get to "lose" is the SP of the unit being merged (even support affinity transfers).
So basically, all you get to choose is :
The IV you want to keep between the 2 units
The SP of the unit being merged
The LV ot the unit being merged (if you merge a lv40 unit into a lv1, it will become a lv1+1).
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