After a flood, it is strongly recommended that a licensed water well driller be hired to shock chlorinate your well if the wellhead has been flooded or submerged even temporarily. A water well driller will have access to more effective products and will have equipment and experience that a typical well owner will not have.
However, if you plan to attempt to disinfect your well yourself, the Alabama Cooperative Extension System has a publication that goes through step-by-step instructions on how to shock chlorinate a well.
Click here for a PDF of Flooded Wells: Shock Chlorination, ANR – 2512.