The sealing and insulation of Rim Joist are handled in the refine/detail section for either the Basement or Crawl Space recommendations.

For basements you have the choice of selecting either “Same as Basement Wall” or “Separately” for existing &/or improved values. If you chose same as, then the rim joist will be calculated at the same R values as the basement walls. Which in the above example, the R value for both would be R 13.

When Separately is chosen, additional fields will open so that you can indicate the R value. This option can be used if you are not insulating the basement walls, and only want to do the rim joist. It is also used when the rim joist have a different R value than the walls.

The Rim Joist option only opens if you are fully conditioning the crawl. A fully conditioned crawl includes the rim joist, crawl walls, and vapor barrier on crawl floor. As with the basement, you can choose either “same as crawl wall” or separately.

Example 2:

If you are insulating the floor cavity (crawl ceiling) the system assumes that the floor cavity insulation includes the rim joist at the same R value as the floor insulation.

References:

Details that connect building components are often the cause of much of the air leakage.

The rim joist or band joist is a particularly troublesome detail. This condition occurs at the basement- (or conditioned crawlspace) to-first-floor interface, and between floors. The concrete foundation-to-wood sill plate connection is often the source of significant air leakage. This area is problematic for several reasons. First, several framing components (sill plate or top plate, rim joist, and subfloor above) need to be connected with sealant as air barrier components; this application is quite workmanship-sensitive. Second, the interior side of the rim joist is a cold surface in wintertime, and has associated risks of condensation.

Though you may not be able to see cracks in the rim joist cavities, it is best to seal up the top and bottom of the inside of the cavity. Also, rim joist air sealing is especially important at bump out areas such as bay windows that hang off the foundation. These areas provide greater opportunities for air leakage and heat loss. Caulk is best for sealing gaps or cracks that are 1/4 inch or less. Use spray foam to fill gaps from 1/4 inch to about 3 inches.

After air sealing the rim joist area it is relatively easy to insulate each cavity with rigid foam insulation or fiberglass batts. If using batts, just cut the insulation to fit and place against the rim joist without compression, gaps, or voids. If using rigid, foam into place. This could also be done in conjunction with finishing the basement, when you would insulate the basement walls floor-to-ceiling. Attic and basement air sealing will go a long way to improve your comfort because your house will no longer act like an open chimney.

Fine Home Building.com: The best Way to Insulate a Rim Joist

Other References:

Building Science Corporation: Critical Seal Application at Basement Rim Joist

EnergyStar.gov: Sealing Air Leaks