Digital BW, The Print

I'm running off a set of prints for a sale this
weekend.  Naturally, this is the time my printer
decides to give me problems...or maybe I created them
myself?

I'm using the MIS 3MK inkset in an Epson R1800...just
finishing off my first set of cartridges.

Part way through printing out my photos and I started
to get some banding in dark areas of the photos.  I
knew I was almost out of ink, so before replacing the
cartridges I decided to drop my MIS cleaning carts in
and run some cleaner through.

I printed about 8 copies of a dark print, until the
page basically came out blank, then I dropped in the
new carts.  I ran several prints, but now the banding
is much worse and I get "overspray" in all the light
areas of the print, including off the sides of the
print, where this is no image.

I did a nozzle check test page and it showed that the
black nozzles were badly clogged.  They have never
failed a nozzle check before, although the Epson
colour inks do from time to time.

I went to do a nozzle cleaning cycle, but I ran out of
cyan ink so it wouldn't allow me to run the cleaning. 
I'm going to buy a cyan cart today and hope that a
cleaning cycle will fix everything.

Now I'm wondering if I did things correctly.  What's
the proper way to use the cleaning carts?  The way I
described above or only during a nozzle cleaning
cycle?

Thanks for any help!

Ken