Query, parameters and permalink

Hi, don’t know if this is the right category, anyway

i couldn’t find these informations, hope someone can help.

1. Where is the documentation for the query functions? I’d like to use wordpress funcs instead of mysql_query but the only info i’ve found are about ordering a query.
I need to use JOIN and IN or equivalent.

Is there an object i need to use to perform queryes?
How do i get the table prefix in case i have to make the queryes my self?

2. the add_query_arg function doesn’t work with permalink
what’s the function i need to use to create relative links to the same site in a plugin so that they’ll work as when using permalink as when don’t

Thanks for your help