ccuell: if this is what is happening to you, then you have done something wrong when you installed your second wordpress installation, as I have 2 seperate wordpress installs on my server and both are using my plugin and they work independently of each other, there is no mention in my code as to what database and/or table to use this is all managed by wordpress itself. Make sure you have a different table prefix setup in your config.php file for each installation and you should have no problems.
apurdam: sadly this is not possible due to a limitation of the query_posts function within wordpress itself, as it only lets you sort on one field not two.
adrianted: posts are unlimitied, if you had 10000 posts they would all show on the sitemap at this moment in time. Have had no requests to limit this until now, but have added it in for you will release it shortly.