How to can my jalapenos? Can you use starsan?

You need to boil the lids to get the seal hot on the inside of lid. You want both jar to be hot so when you screw on lid tight.

I have no idea what's in star-san, but since you have a boiling water bath going anyway, I think it's easiest just to use it for the initial sterilization anyway.
 
The answer to question 2 is DEFINITELY YES; the BWB after packing is safety-critical.  You may want to get hold of the USDA Blue Book on canning (there are a bunch of free copies online), which to my recollection runs down the safety issues to keep in mind with different forms of canning.
 
-NT

Here's the Ball canning website
http://www.freshpreserving.com/home.aspx
 
And some approved recipes for making picked peppers-
http://www.ext.colostate.edu/pubs/foodnut/09314.html
 
Scroll down the page in the 2nd link for a super simple pickled pepper recipe.  Substitute jalapenos for all the peppers listed, use the measurements for vinegar, salt, etc.
 
EDIT- here's the text for the pickled pepper recipe.  There are other good recipes in the link above, check 'em all out~
Pickled Peppers

• 2 pounds Hungarian or banana peppers*
• 2 pounds sweet peppers (in strips)*
• 1 pound cherry peppers*
• 1 Jalapeno per jar (if desired for hotness)
• 1 clove garlic per jar
• 6 cups vinegar
• 2 cups water
• 1 tablespoon plus 1 teaspoon pickling salt
• 1 tablespoon sugar, if desired

*Note: May use a variety of peppers to equal 5 pounds (4 quarts).
Yield: Makes 7 to 8 pints
 
To review the steps of packing, sealing and processing pickled products, see fact sheet 9.304, Making Pickles at Home. For information on canning chili, pimentos or other pepper products see 9.348, Canning Vegetables.
 
Procedure: Wash peppers. Small peppers may be left whole with two small slits in each pepper. Core and cut large peppers into strips. Pack one clove garlic and a variety of peppers tightly into clean, hot, sterilized jars, leaving 1/2-inch headspace.
Combine vinegar, water, salt and sugar. Bring to boil and reduce to simmer. Pour hot pickling solution over peppers, leaving 1/4-inch headspace.
Remove air bubbles. Readjust headspace to 1/4 inch. Wipe jar rims. Add pre-treated lids and process in boiling water for the time specified for your altitude and jar size. For best flavor, store jars five to six weeks before opening.
 
Boiling water bath processing time Jar size Altitudes of:
6,000 ft or less
quart -15 min
pint, 1/2 pint- 10 min 
 
Above 6,000 ft 
Quarts- 20 min
pint, 1/2 pint- 15 min

Kewl! Thanks for the advice everyone. I did look up the blue book usda .pdf that is out there. I guess my only question is, why do you need to do the boil after you pack? (either raw pack, or hot pack method) If my acidity is high, and brine has been boiled, there wouldn't be any reason to boil the whole jar afterward if everything inside is sterile. Is it just for sealing purposes?

According to the extension service publication, nasties can still live in a vinegar brined product so if you cold pack, the jars must be kept refrigerated.  If you want it shelf stable, the jars must be boiling water bathed to properly seal. 
 
"Cold Pack" means covering the veg/pepper with brine, covering the jar and the keeping refrigerated.
"Hot Pack" means pack veg in heated jars, cover with hot brine, lid and ring and then boiling water bath to ensure a properly sealed jar. 
 
Just pouring hot brine over the peppers and sealing with the jar lids is not enough to ensure the jars will seal when the jars cool.
 
EDIT- quote from the CSU recipes-
"Remember, all pickled pepper products stored at room temperature must be processed, to avoid the risk of botulism toxin development during storage. The boiling water-bath processing step can be omitted if pickles are stored in the refrigerator."