I would prefer it be updated in the main query
A select query ("main query"?) cannot update, append or delete. If you need this, you will also need an update query, which will only update the records that satisfy criteria that you provide. If none, every record in the fields you choose to update on will be updated. This query can show what fields would be updated by switching to datasheet view, in which case it won't actually run. However, if the fields to be updated are null, you won't see anything as this view shows what records will be updated, not what the update will be.
A make table query is not the way to go.
EDIT: you could try switching your select query to an update query. Regardless, I'll reiterate what's in my signature - play around with copies of your tables/queries until you're sure all is good.
The more we hear silence, the more we begin to think about our value in this universe.
Paraphrase of Professor Brian Cox.