How do I cover up basement rough in
First take very accurate measurements of the rough-ins and draw a proper diagram showing each of them in relation to the nearest walls. A good diagram will help you in the future but also add value to your house on resale. If I was buying a house and someone mentioned they were covered up I would treat that as having nothing. If someone could show me a diagram and I find one that I can pour water down that may save a home owner a few thousand.
Cut each out below ground level and then fill with floor leveler. If during the cutting process you are opening or exposes a PVC pipe, cap it before the floor leveler.
The other option is to try to hide them in walls but looking at yours, probably won't work.
The pipes here were never expected to be used as-is. Sometimes, maybe, but not normally. So you cutting them will have little to no damage to future use. If people know where they are at and the pipes are in good workable condition under your flooring that is 98% of it.