ok bro first think you need to understand is that creating a BC install you're happy with is no simple feat...trust me. i still have yet to completely accomplish it. if you really want to take advantage of a lot of the bc features out there you need much more than just ships. in fact ships should be last on your mind.
first check out the downloads section sticky "List Of Mods"
http://bc-central.net/forums/index.php/topic,28.0.htmlthat will sorta talk you through it.
now i recommend that since you dont have anything working anyway..uninstall bridge commander..delete the folder..and then reinstall it...just to make sure you didnt screw up anything.
now follow the instructions on the "List of Mods" page
basically downloading and installing one at a time each of the mods on that page, stopping after #36. If one of the links doesnt work it's attached at the bottom of the post.
you may want KM, it's a total conversion, you may not..but start with all of those first. when you restart bridge commander after installing all of this you're going to notice a world of difference. start to try and figure out all of the new features. some are a little strange at first.
now you're ready to start adding ships. try to stick to newer ships/ship packs which aren't BCMP dependent (should say in the requirements), and which can use the SubMenuMod. if they come with an auto-installer it's probably best for you for now.
Feel free to email me if you have any more questions.