It's not too tough, but much easier if you just print the cover pages. Get a photo printer and I'd always recommend a wide format, it will open up more possibilities for you. What matters more than your printer nowadays, is the quality of the image. Ideally, you'd want like a 600dpi scan. Glossy paper works fine for a manual, something like 6.5 mil should be fine. I usually convert any PDF scans to JPG which can be done easy if you Google it, there are some free services. PSX Data Center should have just about anything you'd ever need.
Use good photo editing software like Photoshop, there are alternatives (even free ones) that work just as well. Sometimes you may need to do some adjusting or sharpening of text which you'll find built-in tools for. Sometimes full retyping is necessary in some places. For a standard jewel case book (two pages per side) your image size should be 9.4 x 4.72 length by width in inches. You can make this adjustment easily in your editing software, then make sure in print properties you're printing 100% of actual size, on your best quality settings.
The tricky part is putting pages in them. Unfortunately the thin kind of paper used for pages are among many specialty types only available directly from paper mills and most won't sell them to you unless you buy a lot of money's worth in a bulk purchase. So, I'd settle for just using plain paper for the inside pages. This way you can print on both sides of the sheet like you're supposed to (if you center your image in print settings). You'll need a 9.4 x 4.72 canvas and then just transplant them into place so that they flip in the correct order. For example, starting off with page 2 to the left of center and 14 to the right, and for the flip side of that sheet page 15 to the left and 1 to the right. Once you've folded your pages down the center, they should flip in order, on the back of 1 is 2, on the back of 14 is 15, and everything that goes in between. Measure the center of your prints, then score with a scoring pen before folding to get a nice crease. Finally, staple them all together.
Sounds complicated, but it's not bad.