Most modern operating systems are able to prevent unalignment from occurring. We you format and partition a hard disk or SSD in Windows Vista with hotfix 2553708, Windows 7 SP1 or Windows 8, the OS ensures that all partitions begin with multiples of 1 MB (256 4k sectors) from the beginning of the disk. That ensures a correct alignment. If hard disk manufacturers should transition to even large sectors, you should still be fine with this approach. It's also okay for modern SSD's with 8 kB of 16 kB pages.
Was your hard disk not partitioned with a recent version of Windows, you could potentially run into problems. Windows XP is infamous for this. It starts the first partition at the 64th logical sector, even though a good alignment would require it to begin at the 65th. So installing Windows XP on an advanced format hard disk or SSD will not be good for your performance. Installing a new version of Windows on a disk that was partitioned by Windows XP will also result in unaligned partitions.
Older versions of partitioning software sometimes don't deal with this. Many tools for copying disks also don't address alignment. When the hard disk is larger than the SSD you're copying it to, partitions can potentially end up in the wrong location on the new disk.
You don't need any special software to check whether a hard disk or SSD is 4k aligned. You just open the command prompt, and enter cmd. Then you enter the following:
wmic partition get Name, StartingOffset
It will list the StartingOffset of all partitions, or the position in bytes where the position begins. Take those numbers and divide them by 4,096. If the result is a number without digits after the decimal mark, it means your partitions are aligned perfectly. You can also divide the numbers by 1048576 (1 MB).
The Windows command prompt can tell you whether your partitions are 4k aligned.