You’re correct.
Jefferson issued that statement in a letter to a Baptist group (after he was elected pres.) which was concerned that the fed gov would interfere in the free exercise of religion. Jefferson said he would support ‘a wall of separation between church and state’ to ensure that the fed gov would not get involved in establishing a national religion or regulation of it.
See David Barton’s excellent book, Original Intent, for a discussion and review Jefferson’s complete letter.
And they, the libs, keep using his phrase in that letter but you can’t find it in the Constitution anywhere.