Managing and deploying updates via Configuration Manager
How can i fix this?
Assuming that you want to only have an MW on the Sunday immediately following patch Tuesday, then there is no method built into ConfigMgr to configure this. You will need to either manually create these MWs or use a script to do so. From memory, there are a few similar example scripts posted around the web.
As for the manual installation, that depends on what you mean by manual. Assuming you mean from software center before the deadline of the update, then yes, it will restart automatically in the next MW occurrence after the deadline (also assuming MWs aren't configured to be ignored). If the updates are deployed as available though (it's hard to tell from what you've written what the case is), then no automatic restart will be enforced ever.