Yes, you're right, that's the way row 2 should end, with an open square and one filled square of the set of 3.
The easiest thing to do may be to block off a 6 stitch repeat on the chart which will work for your size. If you start this repeat on the left at the 1&2 line and count 6 blocks over to the right, that's your 6 stitch repeat. So for row 3 you read from right to left beginning with 3 open squares, a filled square, then 2 open squares. You can then continue across the row ending with a filled square and 2 open squares.
Use the chart too to make sure your stitches are lining up correctly with the row below.