You can measure upstage/downstage dimensions using whatever base line you think is appropriate for the show. The reference line could be the front of the stage, the front of the deck, the plaster line, the show portal, or even a prominent line in the deck. What's important is that you include a cover sheet with your focus charts showing where the zero point is, the date the charts were written, and a key to the abbreviations you used.
The Focusing Procedure
To focus each light light, you stand wherever the chart says to. The electrician points the light at you there. If you need to stand someplace downstage of your zero line, then the US/DS distance is shown as a negative number. If you need to be sitting down or standing on something when the light is pointed at you, be sure to include that in the chart.
Once the light is focused on you, the electrician locks it down and begins to make shutter cuts, which are indicated in the body of the chart below the dimensions.
US, DS, TP, and BT can sometimes mean the same thing: For example, a shutter cut on the top of a light may well be the same as an upstage cut. Fill in whatever parts of the chart make sense for each light, and leave the rest blank. It depends on where the light is pointing and what would be clearer to understand. If you're focusing a front-of-house light and you want to indicate a cut off masking borders overhead, you'd probably say "TP Off Borders" instead of "US Off Borders" just because it's more what you want to do.
If you want to indicate Soft or Hard edges, you circle Sf, Hd, or somewhere in between.
If you're using a fresnel and want to indicate Spot or Flood focus, you circle Sp, Fl, or somewhere in between.
If you're focusing a PAR or other light which has an oval beam, then you draw a little arrow in next to "Axis:" showing the orientation. You can also circle either the horizontal or vertical bar or L/R or US/DS instead of drawing an arrow. Whether the orientation is from the perspective of the light or the way it falls on the floor is up to you: just be consistent and include a note on your title page showing which way you did it.
Scenery & Other Oddities
The stand-here-and-focus-like-this method works fine for most acting areas, but it rarely works for things like curtain warmers or template washes that streak dramatically across scenery. For those lights, you sketch little pictures showing what the light looks like on the object. It doesn't need to be overly artistic, but it does need to be clear. Here's a focus chart showing some curtain warmers:
