You can set the full text index to be compressed at a specified time. This is set in the Hyland.Core.FullText.NTService.exe.config file in the following setting:
<setting name="IndexCompressionTime" serializeAs="String">
<value>23:50:00</value>
</setting>
For the value, set the time after which you would like compression to run using a 24 hour clock. The time is approximate and the compression will run after the time specified.