how to upload waypoints

I'm assuming you are trying to upload those waypoints (WPs) in order to add POIs to OSM. That's the only valid reason for wanting to do what you're asking. Do not add WPs to OSM if they are your personal WPs, for example, "My house", Carol's shop", etc.

Because OSM will not accept a GPX file containing only waypoints, I "trick" JOSM into doing this as follows, (I don't know if iD or Potlatch allow this). I upload a GPS trace, any trace will do, along with the waypoints. The trace need not be related to the WPs. To do that I "export" the WPs and the trace in one GPX file using Garmin's Basecamp program by selecting the WP's and the trace before the Export step. Once the file is uploaded using the Open command in JOSM I use the photo_geotagging plugin to utilize the WP data. The waypoints ("markers") will be in a separate layer named "Markers from Selected data ..." and you can jump from one to the other by right-clicking on that layer and choosing Jump to next, Jump to previous. Do not convert the Marker layer to a Data Layer because you will only be using it temporarily as a way to add actual OSM data.

After adding the OSM data represented by the WPs I delete the trace and the Marker layers.