Write down all the collections that you've got, including their sizes and on which hard drive they're located.
Think of which of them make sense, and which could be better divided/combined (if you have enough space on one of the drives).
Choose one of those collections for the start, and create a Calibre library on the same drive where the collection is (this way you can be pretty sure you won't run out of space). If you want to create the library on another drive that the one the files are currently stored on, make space first and copy the folder with collection there (because this way you won't end up, missing space for the books).
Add files in small batches (10-100 files, depending on the size of the file and the amount of free space on the drive), and delete them after adding (end empty the recycle bin).
When you get a bigger drive, you'll be able to combine some or all libraries into one (which is pretty straightforward). That's what I would recommend: I have one big library with virtual libraries in it, and for me, it seems like a much better solution than a couple of separate libraries (at least for now... I like playing with Calibre a lot and keep discovering new solutions and possibilities
).
Do you have back-up of all your files? If not, I would generally recommend buying a new big hard drive / a couple of smaller ones, to have everything in two copies (not because of Calibre, just for safety reasons).