Hmm, you talked about a lot there.

Boundary your fields with SM and your Titan. Import them into Apex or the FW desktop package, into a "main" or "master" layer. Pull in yield maps, imagery, EC maps, whatever to use as backdrops and manually make either polygon zones or sample points sample maps. Export the sample maps back to a card in Shape File format, load the card into the Titan, and you're ready to sample.

Alternatively, as you did above. While at the field, zone out known, visible "special attention" zones into a new boundary or zone file. Import the boundaries to your desktop software "master" layer. Use the boundaries and the zones from the second file to create a new polygon zone sample layer with the special attention zones on it. You can uniform grid the balance of the field after setting out the special attention zones. Export the sample map to a shape file for loading on the Titan and pull your samples.

The steps on this stuff will vary a little from different software packages, as in Apex vs. FW, but the ideas are all adaptable across different applications and different versions even. There is not ONE RIGHT WAY or ONE GOOD WAY to do this stuff. Think about where you want to go in the END, and you can get there.