When my 6 was lowered I had to be a bit creative, even with the lower profile jack my dad had it was too low. I'd usually end up using the emergency jack on the frame rail to lift it up just enough to get the floor jack under it. It was one of those Walmart Black Jack floor jacks, and it was pretty terrible. I think it would have been fine on a lighter car but the MS6 was just too heavy with it and it struggled and eventually popped the seals. Maybe it was just defective, I don't know.
One thing I would recommend is to check the maximum height of the jack, you have to get a MS6 pretty high in the air to get jackstands of decent height under it. I have one of the inexpensive Harbor Freight aluminum jacks and it can lift the car just fine, but even with a jack adapter that gives it a little more height it can barely lift it high enough to get it on the jack stand at the lowest setting. I should have bought one of the low profile 3 tons instead, but the aluminum one is just perfect for the Miata.