Due to the hype surrounding the current high-capacity hard drives, many users are thinking there is something special about these new drives with internal 4K sectors and that they require "advanced formatting" to function properly. Please understand that this is mainly a marketing ploy.
The facts of the matter should all be obvious to anyone with basic knowledge of drives/file systems and the link between them. This article contains some simple brief information on the subject.
What's the deal with the 4K sectors?
A sector is the smallest unit/block of data a drive can transfer. Traditional hard drives have used 512 byte sectors. The plan to change to a larger internal sector size has been in the works for years and now there are drives that are using 4K sectors. The larger sector sizes allow there to be more data on the same platter because there is a gap between each sector (including the ECC data). These drives are still fully compatible with all existing software and operating systems because they (properly) provide a 512 byte sector view and internally handle reading/writing in 4K chunks using read-modify-write. With proper caching technology (built into the drive) the affects of this should be negligible on typical desktops.
What about this alignment stuff?
Alignment has to do with where the partitions and data are located on the drive. Obviously the "optimal" location is where all data to be read/written is contained in the least number of sectors; however, it's marketed simply as aligning partitions to the size of a sector (or block, for devices not using sectors). The reality is you may have a more optimal configuration or setup if the partitions are not aligned to the size of a sector - what matters is where and how IO occurs on the drive, which is dependent on the application's (including OS) use of data, file system in use, the file system driver implementation, and any cache manager implementation.
On the application side of things, one given is the OS paging file which can be heavily used by the OS. The OS will read/write an entire page which is 4096 bytes (4K), so having that file aligned to a sector size is probably the biggest single alignment factor on a typical desktop computer. For that file to be aligned, the clusters of the file system need to be aligned (see below). While we're talking about the page file, if your file system cluster size is less than 4K, you would also want to ensure that the page file is not fragmented or that could affect performance as well.
For the file systems, NTFS clusters (allocation units) occur starting at the beginning of a partition so if that partition is aligned on a sector size, so will a cluster. For FAT the data may not be aligned even if the partition is aligned on a sector size. However, you can use BootIt Bare Metal (BIBM) to format a FAT/FAT32 partition using the Align for NTFS conversion option, which will result in an aligned partition. You can also use BIBM to align an existing FAT/FAT32 partition using its Align option. BIBM is located at https://www.terabyteunlimited.com/bootit-bare-metal/.
However, even if a cluster is sector aligned, it doesn't mean the file system driver is going to read/write entire clusters at a time (in fact, that would normally be a waste of time and slow file access way down). The only time you will see that is if either the file system driver is poorly implemented, or the writes on newly allocated clusters are zero padded (to end of new cluster) for security.
Another factor is a cache manager. If this cache manager reads or writes entire clusters (or multiple of clusters) then having a cluster aligned with a sector size will be optimal for the cache manager and hence anything that uses it.
What's the bottom line on alignment and Windows?
Due to the cache manager and paging file, it's probably best that you align your partitions (particularly on heavily used servers/systems). You can use BootIt Bare Metal to align your new or existing partitions by enabling its global Align on 1MiB Boundaries option (if using independent drive settings, you should also disable Align on End and enable Align MBR End HS and Align MBR HS When Truncated - see the BIBM manual for details) before creating the partition or before using its slide (move) option to move the partition location.
However, if your partitions are not aligned or you don't want to align them, then simply don't worry about it because the system will continue to function. If you find that the performance is not as expected then align them at your convenience to see if that was the cause of your performance issues.