If you get everything you possibly can in the first playthrough (including all the secrets), you'll be missing 1 last upgrade for each skill. These appear on the main path as you go through the New Game+.
Don't worry if you don't find any to begin with - the first one appears about halfway through the game. Here's where they show up:
Dash - Shrine, waypoint 2 - just above the waypoint
Regen - Cemetry, waypoint 1 - above the first switch
Nova - Cemetry, waypoint 2 - halfway to the bridge over the lake
Overdrive - Mausoleum, waypoint 2 - just right of the waypoint
Barrier - Mausoleum, waypoint 3 - just right of the waypoint
Raze - Caverns, waypoint 2 - just left of the waypoint
Bastion - Caverns, waypoint 3 - backtrack down and left to a large rectangluar room
You shouldn't need to search for any of these. They'll be right in front of you as you play through naturally.
The achievement should pop at the moment you pick up the 7th.
PS - I suspect that if you don't get the secrets in the first playthrough, you can collect the missing ones just fine in the second (in which case - first playthrough blind, second with a secrets guide is perfectly viable). However, I didn't test that; personally I got the all secrets acheivement in playthrough 1.