By 1864 the Union Provost Marshals and Missouri State Militia had pretty much driven any outward sign of southern sympathy underground, Montgomery, Callaway and Warren Counties were but a short train ride away from Gariot Street Prison or Alton and the Provost Marshals records from these counties are rife with citizens being detained and imprisoned on accusations by their nieghbors/enemies.
Add in the fact that even some slaveholders and persons of southern heritage (to include Sylvester Baker state legislator from Montgomery County and one of the largest slave holders in the County) were conditional Unionists it's hard to pin down how any one town leaned except by reputation.