Yes, it would be best to wait for a couple of weeks before deleting anything.
Now, regarding your second physical drive: as I understand, the disk was your previous system disk, that is, it contains a lot of information you won't need (all the operating system info and all the programs installed which are now transfered to the new drive) and that takes a lot of space on the disk. So, if possible, you should transfer all your data files to the new drive or an external drive, temporarly. Then, you should format the biggest partition, delete the first two partitions, extend the formatted partition to use the small space released by deleting the two partitions and, at the end, copy back your data files to the new partition.
Sent from my SM-N975F using Tapatalk