Over the years, I've traveled dozens of times in the Superliner sleeping cars' so-called "roomettes" (a misnomer, since the term "roomette" originally meant a quite different type of room for one person only, its recent application to the small two-bed Superliner and Viewliner rooms being an arbitrary and senseless act by the usual Amtrak clods; the older term "Economy Bedroom" was better). My experience has been that even a small suitcase or a backpack is usually excessively awkward to keep in there, and a gym bag is just barely tolerable. So my recommendation would be to (1) bring a garment bag (there's space to hang it) and a small shoulder bag into the room; (2) if necessary, keep a small suitcase of additional items you'll need during the trip in the downstairs storage area (not highly valuable items, though, since the storage area is unsecured, though I should add that I've never actually heard of anything being stolen from there); and (3) check the rest of your things from Emeryville to Denver (free for the first two bags).

By the way, since I've broached the subject of terminology above, let me take the liberty of suggesting that, in discussing features of a so-called "roomette" or other sleeping car room, it makes the most sense to simply talk about "beds" or "bunks", not "berths". "Berth" strictly speaking means "a bed in a special small enclosure made for it". The term makes sense in connection with the "section" accommodations that were common in old-fashioned sleeping cars (Amtrak has no such sleeping cars, though VIA Rail Canada has a few), but it doesn't logically apply to the beds in sleeping car rooms, since those beds are not in individual enclosures of any kind.