One of the greatest tricks that I've come across for setting up a Subdreamer site is the ability to insert a desired plugin into your page designs throughout all categories via mysql.

http://www.subdreamer.com/forum/showthread.php?t=7000

Subdreamer has a table called sd_pagesort (assuming you have used the prefix sd_ for your tables).

If you execute this SQL statement:
UPDATE sd_pagesort SET pluginid='3' WHERE displayorder=2;

Then all existing categories in your website will have the latest news plugin (pluginid=3) placed in your skin's plugin space number 2 (displayorder=2).

For custom plugins you need to add the character "c" in front of the number, so to add custom plugin number 1 to plugin space number 2:
UPDATE sd_pagesort SET pluginid='c1' WHERE displayorder=2;

Works like a charm so long as you can vision what will be where.  Keep in mind if you use multiple design files with different plugin locations, you would need to modify your query.... this example will not consider layout, only which id goes where globally.