We've been asked this several times in the last week. The easiest way is to create a single tournament with both varsity and JV brackets. If you want to keep separate team scores for varsity and JV teams, create separate teams as well.

Use the "File"/"New..." menu and click the [Create from scratch] button. Use the controls on the resulting window to create the varsity brackets. Once those brackets are created, click the [Bracket list] button to bring up the window for adding more brackets. A suggestion is to append "-JV" to the varsity bracket names to get the JV bracket names.  Use the [Move up] and [Move down] buttons to order the brackets the way you wish (e.g. interleaved varsity and JV, all JV first, or all varsity first).

Use the [Team list] button to bring up the window for adding teams. If you want to score JV teams separately, create both a varsity team (e.g. "Ridge High School") and a JV team (e.g. "Ridge High School JV").

When you add or import wrestlers, make sure you assign them to the correct team and bracket (varsity or JV).  From there, it's just like running any tournament.

TournamentSR v7.0.0 includes the ability to disable per-match bonus, advancement, and/or placement points on a per-bracket basis.  If the JV wrestlers shouldn't contribute to the team score, set their brackets to not award any points.