Please have a read of my Mastermind Guide.
To summarise, your additional henchmen are independant of any powers you take. Your upgrade powers (available at L6 and L32) grant new powers to your henchmen.
Common slotting with see nothing added to the L6 Upgrade (and popping a Recharge Reduction in there) and adding two more to the L32 Upgrade (and popping three Recharge Reduction in there).
I did the rather silly thing of adding 2 slots to my levle 6 upgrade before realising it didn't take any enhancements that were really useful to me ^^;
That's what respecs are for 
ok sounds stupid but....
i have just got my 2nd soldier, and it came with equip merc.
do i have to have more slots on equip, or can i now forget about it? and move on with my slots.