Is there a way I can do this?

For example insert a call for a widget in center column of homepage via a php string -- but show that widget content NOT under every single post on the homepage -- but every 2 or 3 posts?

WP 2.9.2
Ata 3.4.6

you could go to ATO->Style & edit CENTER COLUMN->The LOOP and add some php logic to compute the post count then displaythe AD when you want.

Thx JD - that worked very nicely -- and thx to Atahualpa for being such a great theme allowing this customization.
I used

<?php if ( is_front_page() AND $bfa_ata['postcount'] == 2 ) { ?>
my widget here
<?php } ?>

to make this work