The movements were beautiful, all in your ovaries
This is a double entendre that builds on the music/sex metaphor:
1) A movement can be a musical section, that is, “a unit of a larger work that may stand by itself as a complete composition. Such divisions are usually self-contained. Most often the sequence of movements is arranged fast-slow-fast or in some other order that provides contrast.” Benward & Saker (2009), Music in Theory and Practice: Volume II. Note that “Oh Comely” is arranged exactly like this, although its parts do not compose full-fledged movements in musical terms.
2) The different positions performed during the sexual act.
To help improve the meaning of these lyrics, visit “Oh Comely” by Neutral Milk Hotel Lyrics and leave a comment on the lyrics box