Printing decals is pretty easy. I have used the Testors decal paper for ink jet printers, but there are other brands available. Bare Metal Foil offers ink jet and laser printer film. I think you can get some also from Micro Mark.
For practical purposes you can't print white (yes there is/was one out of production, hard to find, printer that does) so you have to work around the lack of white by using white paper. In general, if you were printing a fairly complex decal sheet you might have to cut up your artwork and print some of the images on clear paper and some on clear. For example, if you have writing you probably want to print that on clear so you don't have to cut out each individual letter from a solid white backing. For complex images you can also layer decals on top of each other. I did this with a very complicated image that had to have some white. I printed the black outline parts of the decal on clear and applied it over a portion of the decal with white and colored areas that was printed on white film.
For your white flowers you will need to set a background color around them to print on white paper. I would try to pick a color close to your paint color so you don't have to be quite so careful in cutting them out. You might aslo set up your artwork to make more flowers than you actually need so you have some spares. You can't reuse the decal paper if you need extras so pack as much stuff on a sheet before you print it out.
Any decent paint/draw/photo program can be used to edit your artwork. I use Gimp 2 which is a free download but I have also used Paint Shop Pro which I bought at Target for about $70.
Print your image first on paper to make sure its working right, the right size etc. Then slip in a sheet of decal film. When the printer ink is dry, you need to seal the ink. You can use Testors clear decal fixative spray, Testors Clear Gloss Coat, Tamiya Clear Gloss, etc. Spray a couple of LIGHT coats of clear on the decals and let dry between coats.
Then carefully cut out the decals and apply.
The original Snoopy decals may have actually been stickers. You can also print your images on Avery full sheet self adhesive label paper or some printable vinyl stuff for DIY bumper stickers.
I printed these Aurora scanned decals using Testors paper
This is the original, scanned, sheet with a lot of yellow and also some color mis-alignment
These two images show how I cleaned up, and recolored the images. You don't have to edit each individual duplicate image. Fix up ONE then cut and paste it back onto your artwork for the required total number needed.
The original red ares were not good so I totally removed the red and drew it back in again with Gimp