Merge,Stamp or Flatten

[ameerat42]

I am ? sure if I understand you...
If you want to SAVE layers, you should used Photoshop's PSD file format.

But, if you just want to save the file for display as a jpeg, then just Flatten the layers.
The Merge command "merges" layers, and layers to the BG. Sometimes, though, Merge
still requires that you Flatten the image (but not always).

But "best" as in what, because the layers are still flattened?

[Kevvy]

Sorry I should of been clearer about what I'm doing.
its the final save and conversion to TIFF for print output.