There are just as many pasta alla vodka recipes that advocate adding the vodka at the end of the cooking process as there are that insist it should be added partway through. For me, the best way to draw out that peppery taste and balance the sauce is to add the vodka partway through the cooking process. This enables the alcohol to burn off - rather like the addition of wine to a risotto. For this reason, I like to add my vodka after frying the shallot but before adding the tomatoes. It's really a matter of personal preference, so if you lean towards enjoying a more pronounced hit of alcohol in your pasta, then by all means stir it in at the ned.