When you first create replicas and your main database is the Design
Master, all your tables, queries, forms, etc are replicated. When you
then create a new query, when you are asked to save, there should be a
check box that says Make Replicable. If you check that box, and then
sync your replicas, those queries will appear in the replica. You can
tell that something will be replicated by the icons. If there is a
yellowish icon with two arrows, then it will be replicated. If you
have queries without the icon, don't fret, you can still make them
replicable. Right click your query and select properties, there should
be a checkbox that says Replicable. Check the box and close the
properties window and the icon should appear.
Hope that helps!