1. Put 1/2 or 3/4 inch wide masking tape down on both the shower pan and tile about 1/4 from the corner you want to caulk.
2. Apply the caulk (don't worry about getting it uniform now) and spread it along the joint with a DRY finger so that it's more or less uniformly distributed.
3. Pull off the masking tape so that you have a more or less uniform amount of silicon caulk along the whole length of the joint. Give the silicon a good 10 minutes to skin over.
4. "Tool" the joint with a finger dipped in a 50/50 solution of liquid dish washing detergent and water. Dip your thumb, forefinger and middle finger (and even ring finger) in the soap solution and wipe the joint for about 6 inches with one of your soapy fingers. The soap will run off your finger onto the silicon, so you can't tool very far before the soap runs off and the silicon starts sticking to your finger, at which point you start making a mess. So, only do 6 to 8 inches at a time. After each 6 to 8 inches, rub your fingers together to redistribute soap over all of them, and do another 6 to 8 inches. Keep doing that until you've done the whole length of the joint, redipping in the soap solution frequently. Once you've done that, you'll have a film of soap over the silicone, and you can run your soapy finger all along it's length without stopping to help smooth it. Don't press hard or you'll gouge it out of the corner.
5. Let it cure overnight, and you can shower the following day. It still won't be hard, so watch where you put shampoo bottles and such, but within 2 days it should be close to it's full hardness.
6. There are different kinds of mildew resistant silicone caulk. If you can, get either Dow Corning 786 or GE 1700. Both of these will cost about 50 percent more than the standard stuff, but they have better adhesion and more mildewcide in them. If you can't find these in the home centers, look in your Yellow Pages under Caulk or Caulking Equipment & Supplies. Most places will sell to you because they don't sell to retailers, they sell mostly to caulking contractors.