Although the Seven Lakes Trail can be hiked as an out-and-back round trip from either trailhead, it's often done as a short thru hike. There is no public transport between the two trailheads so you'll need to set up your own car shuttle, and you might want to start at the Engineer Lake Trailhead, to be certain both cars can reach it along rough, little-maintained Skilak Lake Road.
With that said, Kelly Lake Trailhead is the easiest to reach, and even if you just hike from here, you can enjoy some beautiful walking along the shore of Kelly Lake. There are also spur trails (off the main Seven Lakes Trail) leading to Hikers Lake and Hidden Lake.