Advice Please, Before I Spend.. Scanning & Printing.

My wife paints watercolour portraits of animals and likes to keep copies of them before they go to the customer. She would also like to sell prints of the paintings but I cannot get decent prints with my equipment. Definition is lost no matter what resolution I scan and print at, some darker colours disappear and other colours change. I spoke to a guy at Canon today, and he said that the colour information read by the scanner was more important that the resolution, and with what we have gleaned ourselves we have come to these conclusions : We need a better scanner, a 48 bit, mine is a cheap Epson 1260Perfection which is 16 bit. We also need a decent printer which has multi-colour tanks. My wife was told that we won't get decent copies of graphic work with a 3 colour printer. I have a Canon iP5000 which does a great job on photos, but whether the prints of the paintings are also affected by the printer as well as the scanner, it's hard to say. We have tried a couple of pro print shops, but results have also been a little disappointing and their prices make the sale of prints unlikely. I was thinking in terms of the Canon Pro9000 printer as it takes A3 size which would be useful for other jobs, and an A4 48 bit scanner. Any thoughts, does this seem sensible? I've been told to address the software first, but I really don't know what is meant by that.. I assume it's matching the monitor to the printer, but I glaze over when I try to understand it! I've just checked the spec. for my Epson scanner and it reads, '16 bit per pixel per colour internal, 8 bits per pixel per colour external'. Confusing, or what? No idea what that means..!
Ah-ha, after much searching, I've found a good site for dumbo's like me which explains scanning and bits, etc. it's at Scanning Basics 101 - All about digital images. I think I knew it once, but memory decreases as time increases!