1. For the general question of what alignment of a SSDs means I recommend Google - especially Wikipedia.
2. Secure Erase cleans the SSD of all data which speeds up future Write operations. It does the same as Trim and Garbage Collection except that you get an immediate clean SSD rather than a cleanup over time. This article explains what happens: Garbage Collection and TRIM in SSDs Explained - An SSD Primer - The SSD Review
3. If you do a clean install, the Windows installer will align the SSD automatically. If you want to make sure that the 100MB system partition lands on the SSD, it is advised to disconnect all other disks during the installation. Why? - because the installer has the habit of placing the 100MB system partition on the disk with the lowest port number - and often that is not the SSD. Should you have the mishap of the 100MB system partition (and thereby the bootmgr) landing on another disk, I suggest to move the bootmgr to the C partition on the SSD. Bootmgr - Move to C:\ with EasyBCD
. In fact I always move the bootmgr to C in all cases because that makes imaging and recovery a lot easier.