When designing a spaceship, various frames of reference are possible, but two are common: the main thrust direction can either be labelled "up" or "forward".
NASA usually uses thrust-forward [1], but the LEM was thrust-up. Russian craft always seem to have been thrust-up. I have no idea about Shenzhou. In fiction, Lost in Space was thrust-up while Star Trek and Star Wars are generally thrust-forward. It doesn't make much difference, for the most part, but it does make some. For one thing, seats seem to end up raked slightly differently.
For larger vessels (fictional or planned), it will probably make more difference: thrust-up is probably better, because when thrust is activated things will fall in the "down" direction; it's easier to reason correctly about that. With thrust-forward, things will fall "aft" — counter-intuitive, possibly dangerously so. For instance, a passage parallel to the thrust vector will be labelled "up-down" in thrust-up orientation, obviously wrong or at least in need of safety arrangements (railings). In a thrust-forward orientation, it'll be labelled "forward-aft".
[1] NASA-STD-3000 I 8.5.3.2 Directional Designation Design Requirements
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