WD's free utility is called Acronis True Image WD Edition and it can do LOTS of good stuff, including cloning. BUT it will only make a clone TO a WD drive - they are happy to help you move all your data to one of their drives, not a competitor's. A complete clone, by the way, will be EVERYTHING - OS (all files in the right places so it can completely take over as your boot device), applications, Windows Registry, data files etc. Thee is NO need to copy anything else manually after.
If you buy a new HDD from Seagate instead, their utility is almost the same and it's called Disk Wizard. If you buy a Samsung Spinpoint, check their website first to see if they offer such a free-download cloning utility.
As I said, a cloning operation would copy EVERYTHING from source drive to destination. However, you asked also a general question of how to copy a file from a "storage hdd" to a "boot drive". You do that exactly as you would do any other file copy. Make sure the receiving drive has a place for the file (that is, MAYBE you want to create a particular folder to put it in, but maybe you will put it into an existing folder). Go to the source drive and find the file(s), highlight it (them) and press CTRL-C (keyboard shortcut for a Copy operation). Or, right-click on the file and choose Copy. Now go to the destination drive and find the folder where you want it to go. Click on the folder name, then press CTRL-V (keyboard shortcut for Paste), or use the top menu line to choose Edit ... Paste. This will COPY the file(s). If you want to get rid of it on the old location, go back there and Delete it. You can combine these two operations into one. Right-click on the file and choose Move instead of Copy. When you Paste it in the destination, it will be deleted from the source.
You can always highlight files, then hold down the right mouse button while you drag them to the new folder. When you release the button you'll have a choice of whether this is a Copy or Move operation.