If filters are defined at the server, domain and user levels they are applied in this order and if the messages matches more than one rule the last action is applied.
For example, in a scenario where a rule was defined at the server level, one at the domain level and one at the user level in the Axigen log file you will find the following lines:
Start processing the message
First the message is filtered by the rules defined at the server level:
Next by the rules defined at the domain level
Finally by the rules defined at the account level, in this case the account is postmaster@domain.tld:
The filtering process ends.
If, for example, after filtering the message with the server level filters the message is going to be delivered to "Spam" folder and then the message matches the conditions set for the account level filters and the action for the account level filters is to deliver the message to "Trash", then the message will be delivered to "Trash" folder.