We created a new Monthly deployment for August 2015 updates on 17th Aug 2015 

This was targeted to our servers.

On 18th  a new critical patch came out so i though i would add that in as well. 

Our deadline was on 19th August.

However what happened in our case is on 19th all machines installed the updates and rebooted , however the Single update we added on18th only got detected after the reboot.

I assumed that when i added the update on 18th , it will be included in our patch window on 19th and a single restart will be needed.

Now i have all our machines waiting for installing this single update.

I am afraid that when i approve updates in September, I would need to reboot 2 times. 1 for the Aug 18th patch and then 2nd time for all Sept patches.

How can i make sure they get installed in the same go and only 1 reboot is required.

Only in rare cases will you need two reboots for a SU. Your Aug. issue was likely a timing issue.