Hi there,
Some of your questions have already been answered, but I'll probably cover those topics again just 'cause I'm in the neighbourhood.
Masking.
You have several options here.
There's the old standby masking tape, and its low-tack counterpart painters' tape. In both cases you have to be very thorough in application, to make sure you've got all the curves covered and masked, and that the edges of your masking are well burnished down so they won't lift while you're laying down paint. In the case of tape, you'll invariably have sections with differing numbers of layers in place, and if you're cutting the tape in-situ it can be challenging to get through all layers without too deeply scoring the body. Paint bleed can easily occur with tape; apply paint in very thin layers so it can dry before it has a chance to creep anywhere.
Next is vinyl mask, either in sheets you cut yourself or in precut designs. You still have to make sure it's stuck down thoroughly, and while paint bleed can still happen, in my experience it's far less prevalent. Most low-tack masking vinyls tend to be fairly easy to cut.
Lastly, and my personal favourite, is liquid mask. This is a thick latex-like gloop that you can paint onto your intended surface, and when dry it cuts and peels very cleanly and easily. You can brush it on, or thin it a bit and spray it on instead. With either method, you will have to do multiple thin layers to be sure it'll be thick enough to peel without just breaking with each piece you grab. Test with tweezers; grab and pull - if it "tents" without breaking too easily, it should be thick enough to work with. You of course want it to be as thin as possible, so it'll cut easily. The balance point isn't too hard to find; do some tests in an unused section of the plastic. I very much prefer spraying liquid mask, but if you've never worked with it before you should probably brush it on - just be sure to smooth out your brush strokes as best you can, and apply in thin layers, letting it dry between coats. Again, test at each coat to be sure it'll pull up without breaking too easily.
Painting.
The standard rule is to paint your darks first, then lights. You need your paint only to be as thick as is minimally required to be bright and even while on the chassis and viewed from above - hold it up to a light and depending on the colour you'll probably be able to see right through it. This is the reason for the standard dark/light rule - paint dark behind light and it'll ruin the lighter colour. This rule of course can be broken, but it's not recommended for your first few works on clear plastic.
Once a layer is down, say black for example, you can ignore it for further colours - you don't need to mask it like you would have to in the case of a boat or ABS car/truck body. Such is the magic of clear plastic.
When spraying apply the paint in light, thin coats. You want it to be in the process of drying as soon as it lands - this will give it no chance to run or to bleed under your masking. In most cases, apply just enough coats that the colour is thorough and even. This is of course a rule that is meant to be broken, but I don't recommend it for your first few pieces. You can easily test to be sure if you like; set the body down over a high-contrast item and judge for yourself how opaque you like it. I use a tablecloth with a black&white checkerboard pattern.
Practice!
There are millions of words on the web about painting, and millions more photos.. but when it comes down to it the most effective teacher is experience - even a little bit goes a long way. Get yourself a couple empty clear plastic soda bottles; rinse them out, cut them in half lengthwise, and practice your process on those. It'll give you a sense of just how your materials are going to work for you, and make the first body you work on that much easier and more fun.
This is probably a good idea in reference to your striping paint question as well; adhesion might be an issue. Lay down some stripes, back it in another colour, let it dry, and give the test plastic a bit of a flex to see if the stripe flakes away.
If you've painted "forward" before (on the outside surface of boats I think you mentioned), then really the biggest hurdle is learning how to paint "backward" (on the inside of clear plastic).
I hope this is of some help. Have fun!