Can I use a junction box where a sub-panel feeder will exit my house?
Even better don't run ANY wire yet.
Just run the conduit now. Add the wire later, once you figure out exactly what you need. Just make sure the conduit is big enough. You'll need 3 wires if you use metal conduit (hot/hot/neutral), 4 wires (hot/hot/neutral/ground) if you use PVC. There is some downsizing permitted for ground and possibly neutral. If you go with 1&quot; EMT then you are OK for 3 x 3 AWG copper for 100A. If you go with 1-1/4&quot; EMT then you could use 3 x 1 AWG aluminum for 100A.
As far the actual junction box question: You can certainly have junction boxes in between sections of conduit, and switch between wire types. You can also have (but probably doesn't make sense here) cable inside without conduit and transition to wires inside conduit for the outside run, or conduit inside with wires and transition to direct-bury for the outside.