How do I build my basement bathroom so that it aligns with existing in ground plumbing?
Depends how it was installed. In many cases, the &quot;standard procedure&quot; is to cut the concrete open so you can get the &quot;roughed in&quot; (i.e. roughly positioned) pipes connected to exactly where you want them. Depending exactly WHAT was roughed in, you might need to do that so there IS a trap on the shower, for instance. The roughed in pipe may not have one installed, and unless you are raising the floor the shower/tub trap has to be under the floor level.
Concrete can be cut, drilled, and broken up as and when needed.
If you open the pipe up and carefully (don't drop anything in) shine a light down there, then pour a quart of water down the presumed shower/tub pipe, you should either see standing water (and the smell will stop) or you won't, and it won't. That will tell you about the trap situation. It probably won't have a trap full of water if it's been roughed in a while, even if there is a trap, so you need to add the water and see if some stays, or not. The toilet and sink/lavatory drains would not have underfloor traps.
If you do have a trap on the shower/tub drain, then you would need to choose the specific shower/tub you are going to use based on where it is, and how you will construct the walls, remembering the thickness of all layers, and build to suit - or cut the floor and adjust anyway.