Q: How do I go about getting intrastate authority? Does it have to be yearly or can it be a trip per trip thing?
A: In response to your question, the immediate answer is yes, like any other permit it can be obtained for specified time period other than annual.
Let me offer you some options to gather additional information. As you know there are a number of companies who perform the service of applying for intrastate authority and of course there is a fee and the fees range according to the company and the level of permit authority being sought in addition to the state fees. I would suggest starting with the FMCSA web site and reviewing 49 CFR parts 350-360- and 390 which covers intrastate applications.
I would imagine each state has some entity that you can apply to direct for example with the Arizona Department of Transportation we have the Motor Carrier and Tax Services section within the Motor Vehicle Division that handles the applications. I don't have the fee schedule but I can tell you Arizona fees are based on the time period required for the authority (i.e.:single trip, 30-60 days, annual) and the type of commodity being transported.
I know it's a simplistic answer but intrastate authority is a broad topic and it's hard to capture much of the details in an E-mail response.
I hope my answer provides some guidance. I have provided two Internet links for the FMCSA web site and an ADOT form to submit inquiries for permit applications.
 FMCSA Web site: http://www.fmcsa.dot.gov/rules-regulations/
ADOT Commercial Vehicle Permit Inquiry Form: http://mvd.azdot.gov/mvd/formsandpub/viewPDF.asp?lngProductKey=1821&lngFormInfoKey=1724