using the flat side of your notch trowel; fill the 'divots' / lugs in with thinset. Hold your trowel tight against the tile. Always hold your trowel at approximately a 45* angle.
When I was in Florida, the slabs were fairly flat, as best I can remember and that has been some years back. Now, I'm in South Carolina and I can't find a flat slab.
Using a large format tile will accentuate any uneveness in your slab.
Periodically lift and check the back of your tile to ensure that you're getting a good bond transfer.
Custom Marble and Granite Mortar mix or a similar non-slumping/sag mortar works well with large format tiles.