NCC options are available in the NCC Preferences (in menu File / Preferences... , "Tools" section, "NCC" tab).
We recommend hierarchical over flat comparison because hierarchical comparisons are faster and the mismatch diagnostics are much more precise and intelligible. However, transistor size checking limits what NCC can compare hierarchically because the size of a schematic transistor may depend upon the instance path.
The best way to use NCC is to initially perform all your comparisons hierarchically. This will typically require many iterations. Once you have gotten your cell to pass a hierarchical comparison, turn on size checking. This will report transistor size mismatches.
NCC does the following when size checking is enabled. After each topological comparison, NCC checks if it found any topological mismatches. If NCC found no mismatches then NCC checks, for each pair of matching transistors, that the widths and lengths are approximately equal.
The two tolerance values allow the user to specify how much more the larger of the two matched transistors may be than the smaller before NCC reports a size mismatch. The "Relative size tolerance" is the difference in percentage. The "Absolute size tolerance" is the difference in units. NCC reports a size mismatch when both tolerances are exceeded.
If you choose "Check transistor sizes" and "Hierarchical Comparison" simultaneously then NCC restricts which cells it treats hierarchically to ensure a correct answer in the presence of automatically sized transistors. For this case it compares a pair of cells hierarchically if and only if each cell is instantiated exactly once.
It is occasionally useful to continue checking even after mismatches have been detected. For example, the designer might find that although a cell mismatches, it cannot be fixed because someone else designed it. When asked to continue, NCC will do the following when comparing cells that use the mismatched one:
The check box "Don't recheck cells that have passed in this Electric run" skips the checking of a pair of cells if they have ever passed in this run of Electric. Because this command is not smart enough to recheck the cells after either have changed, this command is of very limited utility. At the moment NCC has run sufficiently fast that it doesn't seem worth the effort to implement anything more sophisticated.