About the reboot:
BigFix dose not automatically reboots your system once the patches are been applied, while taking the patch deployment action you will see a tab names post action, if you select “Do Nothing After Action Completes” will avoid the automatic reboot of the systems. And later when the action gets completed you will see the action status as pending restart that means the system requires a restart.
About the Manual patching:
BigFix works on a simple term called as relevance, which will tell you which patch is applicable for a particular system, that includes kernel level patches and application based patches. I have not encountered any script which delays the patching in BigFix. If you want to deploy the patches manually you can deploy it manually it wont effect BigFix platform but applying patches manually will consume your time.
With the help of the relevance BigFix finds and shows you the applicable patches only.