how to prepopulate a flexifield in form_alter?
do a form alter and add your value as a default value using the default value key,

http://api.drupal.org/api/drupal/developer--topics--forms_api_reference.html/5#textfield

'#default_value' =&gt; //my value; 


you can always print $form in your form_alter after you have altered your $form, to have a better look at your flexifield array, and chck if the default value is set like it is shown in the forms api reference link above. :)