Our cement was fairly smooth (which was why it was so slippery). If you're just laying the cement now, I would suggest you make it fairly smooth, but you have to let the cement cure X days before you can put on the epoxy. The smoother the cement, the easier it is to clean... even new cement will require cleaning before application.
You could actually phone the company and talk to them - we found the company to be extremely helpful and informative.
I am using straight edge mats, not interlocking, and I got the 3/4 inch thickness. I have experience with this in several boarding barns and have not encountered problems with curling edges. I am insetting mine because it makes sweeping much easier. My barn will have similar traffic to what you describe for yours, so I don't expect heavy wear.
I have the same set up. Regular heavy duty stall mats, cut very accurately and tightly to fully fill in the entire barn aisle. At the cross tie area, my husband put in Concrete screws to screw the mat to the concrete below to keep the mat from shifting at all. Works great and looks very good after 6 years of horse traffic. We regularly scrub/wash them too and they look still like new.
I have sand aisles in my barn. White masonary sand (NO rocks, pebbles, etc - it's like beach sand). I did this out of neccessity as we walk, jog, and break babies in the enclosed shedrow. I have a friend with a small backyard 6 stall barn and she went with sand also after seeing my barn.
We rake it daily (the same as you'd sweep concrete aisle) and water it once/day when we fill water buckets to keep the dust down. If it's sales prep time of year where we are walking horses all day long, we'll water it a 2nd time after lunch. I have a steel barn so we hose the door fronts off daily too to keep them white and pretty.