At this point, I've only used a combination of Tcl and SQL to query a database.
IMHO, I think it's irrelevant which languages you're using, things are really going to get confusing if you've got a mix of scripting, markup and SQL unless you format everything to the point of excess.

Have a look at Philip Greenspun's SQL for Web Nerds, particularly the style section.
It's all Oracle8i stuff, but it should apply to anything with SQL.

When I've coded scripts with large SQL queries, I often put the query into a string:

my $query = "SELECT post, post_time, user_id, post_id 
             FROM my_table
             WHERE post_time > sysdate + 1
             ORDER BY post_id;";
[download]

Even if you don't like my idea of having the query seperate, or it's impossible, then just get used formatting the queries so that they stand out from the Perl and are readable as SQL.

Hope that helps,

BazB.

Update: Seems like a slight more Perl-y way of doing this might be to use HERE documents, as described in this node by steves.

Further update: fixed the link to SQL for Web Nerds