I'm assuming here that you're doing a black and white strip, and that any coloring will be done on the computer.
Open your template, select your white background layer, and leave it open. Scan your artwork at 300 DPI in black and white (unless, of course, you're scanning pencils or color, in which case you'll scan in grayscale or color, respectively--if you're scanning color you'll also change your template mode to color). If need be, rotate the canvas on your scanned image. Using the marquis tool, select the area of your artwork, switch to the nudge tool, and drag your selection into your template. Position and resize elements if you need to at this point.
Cool! You've got your art into your template! Resize your frame layer(s) if you need to, do any computer coloring you have planned, and what you have should look like a "real" comic, minus the dialogue and word balloons. Save this to your Raw folder as a PSD document, using the following naming convention (this will be important when we get to posting and updating later, assuming you're using Walrus as your update script--I had to change the names of all our comic files before we could launch, and it was frustrating): YYYY-MM-DD.psd
YYYY, MM, and DD are of course the year, month, and date you plan for this strip to run. The document you've just saved will be your working file. (Of course, if you end up using a different update script than the one we use, it will probably have it's own naming convention.)
We covered why you should scan and work at 300 DPI, but why save a 300 DPI version if you're going to be posting at 72 DPI? Well eventually, if you get a large enough following, you may want to put some of your strips on T-shirts or other merchandise, produce a printed book, or get syndicated to newspapers. 300 DPI is pretty much the standard there. You may also eventually want to make some changes to older strips. Resizing from 300 DPI to 72 DPI works well, but trying to resize from 72 DPI up to 300 DPI will give you ugly results--you can always size down, but sizing up will not recover teh lost information. Remember, just because it looks good on your monitor doesn't mean it will look good in print.
(But we did your template at 72 DPI and resized it to 300 DPI, didn't we? What's up with that? Well, we didn't have any artwork in it yet, so there was nothing to get mucked up through resizing.)
Save your work.
So now you've got your 300 DPI comic, but no dialogue, and the title and other text info are probably in an ugly font. I've waited until now to discuss foint choices because you'll want to play with some fonts to see waht actually looks good with your artwork. Fortunately, there are some great resources online for free fonts.