Suggestions:
1. Picture of problem would help? (Are you able to post pictures on 986forum?)
2. Keeping all your questions about the project on one thread would also help as people will have context and no need to repeat all the project details?
This also helps organize the forum better to keep posts related to one topic (e.g., questions about your suspension lowering/service project planning and specific help questions) to one thread. It could avoid having all these threads seemingly related to your current project consolidated into one:
http://986forum.com/forums/general-discussions/62962-couple-more-questions-rear-lowering.html
http://986forum.com/forums/general-discussions/62955-nut-size-bilstein-hd.html
http://986forum.com/forums/general-discussions/62932-lowering-rear-boxster.html
http://986forum.com/forums/general-discussions/62756-drilling-out-easy-out.html
http://986forum.com/forums/general-discussions/62746-front-strut-help.html
http://986forum.com/forums/general-discussions/62699-strut.html
http://986forum.com/forums/general-discussions/62719-spring-question.html
http://986forum.com/forums/general-discussions/62661-stahl-wille-sf12623-two-stage-tie-rod-tool.html
http://986forum.com/forums/general-discussions/62667-spring-removal-hail-mary.html
http://986forum.com/forums/general-discussions/62564-springs-por15.html
http://986forum.com/forums/general-discussions/62336-lowering-2000-s-help.html
(Note that I'm not suggesting you not ask for help, but consider organizing those questions better into a related thread, to make the forum organization better and also allow contributors to better understand the context of your questions.)
To answer your question about removing the nut (this is not a "bolt"!) on the ball joint, I would not hesitate to put a properly fitting closed-end wrench on it, and give it a good whack with a BFH (big *** hammer.). If the nut turns without loosening, that's a different problem which can be addressed by either inserting into (and counter-holding against) the threaded shaft using the properly sized Allen wrench, or putting a floor jack under the ball joint and applying upwards pressure to provide some additional friction in the ball joint (to help promote the ball joint shaft keeping still). The spherical bearing on the end of the toe arm is called a "rod end", by the way, not a ball joint.
If you have successfully removed the nut, then you could use a ball joint separator tool. This low cost one from harbor freight fits the rod ends perfectly (but will need some enlargement of the inside diameter to properly fit the ball joint). Grease the threads and the metal to metal contact points with an EP (extreme pressure) grease, and push it in fully against the rod end or ball joint (so you give the ball joint removal tool as much leverage as possible.)
http://t.harborfreight.com/3-4-quarter-inch-forged-ball-joint-separator-99849.html?utm_referrer=https%3A%2F%2Fwww.google.c om%2F
Other tools you could use are something called a pickle fork, but they will damage the spherical bearing's rubber boot, and necessitate new parts replacement. (The joint removed with a pickle fork should not be use-used because the boot will get damaged.) I would recommend a properly fitting ball joint separator instead of a pickle fork.
Best of luck!