OK, you seem to already 'get' most of it, but let's work up to finding TDC for Speeduino, so we are on the 'same page'. This is how my brain sees it, so I will use some of my previous posts to describe it. Review
this, then review the linked page in it to
here.
If that is making sense, you can see that positive numbers are the crank rotating past TDC to find Tooth1, and that negative numbers are the same position, but on a different stroke or cycle. This makes no difference to crank-only setups, where wasted-spark and multiple injections-per-cycle are used, as every crank rotation is seeing spark and fuel at the same points across all cylinders. No worries.
However, and to extend the effect of + and –
Trigger Angle, for (example) full sequential with a cycle ("cam") signal, using a positive or negative number will change the beginning of the 4-stroke cycle to the other crank rev of that cycle. This actually changes Speeduino's understanding of the position of
TDC Cyl1 compression stroke to a different cylinder,
or Cyl1 on a different stroke. This begins the cycle to make injections and sparks in proper order in the 2-rev 4-stroke cycle. I hope that makes sense, and partly when it would make a difference.