rbaxter1 - which operating system are you using? With NT/2k/XP you can't copy all the files while the system is running (a number of system files are in use, and are not accessible). 9x/ME should be able to copy all files, apart from swap file I think (which you don't need anyway) - but it won't have a boot sector unless you create one first (run sys x: if already formatted or format x: /s if not).
I don't know what you mean by 'issue copy command'. You'd need xcopy with various options set if copying from dos/command line - but you can copy using explorer (copy/paster, drag and drop) as long as options showing all hidden and systems files set.
Best way is via a disk/partition cloning software like Ghost or Drive Image (especially if you intend booting from new drive).