Modeling BNSF and Milwaukee Road in SW Wisconsin
According to the NEBW Guide to Rolling Stock Paint Schemes on the Rensselaer Railroad Heritage website, the map logo was used between 1940 and 1947. In 1947 the map logo was dropped and "Ship and Travel all the Way" replaced the map logo.
The color guide doesn't mention any color for the underframe and trucks for the mineral red boxcars so I am assuming they were mineral brown like the rest of the car. The photgraphs with the article are inconclusive due to shadows and dirt.
It does say that reefers had black underframes and trucks.
Now here is what's interesting. It says that after 1930 through the 1950s that the roofs of the mineral brown boxcars were painted black with metal running boards unpainted and wooden running boards painted the body color.
The info is available here: http://railroad.union.rpi.edu/index.php?title=Rensselaer_Railroad_Heritage_Website It is a subscription website but it's full of steam and transition era information.
As usuall, Jim has some good info. Another source I would consult is the Steam Era Freight Car Modelers Group (STMFC) at yahoogroups. There are some very knowleable freight car modelers there and some that model the Santa Fe too. https://groups.yahoo.com/neo/groups/STMFC/
You'd have to get approved as a member but it's painless.
It is possible that the underside of the cars was painted the same mineral brown or black as the practice varied by road and sometimes changed over time.
Victor Baird
From Richard Hendrickson's "Santa Fe Railway Painting and Lettering Guide For Model Railroaders Volume 1 Rolling Stock":
"Mineral Brown--sides, ends, and doors; underframes and trucks on repainted cars...
Black--underframes and trucks (new cars only)..."
That leaves you with one teeny little question, of course.
Ed