If you can avoid it, keep beams and joists from going through your continuous “red pencil line” airtight layer. A simple approach is to run your airtight layer over your ground floor (tape the plywood), and under your roof (taped vapor variable INTELLO membrane under the beams). However, if you have a floor within your thermal and airtight envelope, you would still need to deal with the joists that carry this floor.
In new construction you can and should design the airtight layer to avoid these issues. You can wrap SOLITEX membrane strips around the joists as shown above and to the right. Of course you need to plan ahead to make sure that (1) the membrane is installed before the joists are set, and (2) the membrane is wrapped around these joists (optionally around the rim-joist too) and over the floor before the 2nd story wall is built. It can be durably connected with TESCON Vana tape when the interior airbarrier (Plywood, OSB, INTELLO) is installed.
Another approach is the method described by Gregory La Vardera on his LamiDesign blog. It simply continues the airtight layer straight down along the inside of the service cavity and uses a ledger board to carry the joists – avoiding any difficult wrapping of membranes around joists. These straight runs reduce complications and chances of errors – resulting in tighter houses and allowing you to get below 0.6ach50 without too many sleepless nights.
Because the heat flow parallel with the grain of the wood (as is the case with a joist) is about 3 times as conductive – 0.38 W/mk, R-0.37/in) compared to 0.13W/mk, R-1.1/in for across the grain – there is an added benefit to keeping the joist ends as far away from your insulation layer as possible. Putting the rim joist behind some insulation (as in the 3d image), combined with Greg’s solution, prevents a good amount of thermal bridging.