A thing a have used before was adding CEP2 to the app_config file. That way you can allow boinc to download plenty of wu's (if available) but the config file will limit the number of wu's that can be run at one time.
Limiting the number of wu's in the device profile at wcgrid.com will allow boinc to only download new wu's when the first are finished. And the new ones will be place at the bottom of the cue.
I had this in the app_config file.
Code:
<app_config>
<app>
<name>cep2</name>
<max_concurrent>2</max_concurrent>
</app>
</app_config>
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