Root apps on SD card not on phone after ROM flash

[CleveRuse]

1. ok, so i'm a newbe as this is my 1st droid(thunderbolt),my 1st experience w/ all things root and my 1st post so please be patient. i've many questions but shall start w/ this(not sure where this post belongs so please hep me out.) i have root access and downloaded the 1st ROM i saw from ROM Mgr and ended up in a boot loop tho i believe my previous ROM was backed up(i would l8r realize the new ROM prob. was't specific to THUNDERBOLT but not sure why i cant go back to old). . .it did load once during which time i lost root access, then got stuck terminally. So i flashed the 4DLTE EXTEME on my SD card and it worked. and says now i do have root. now i stiil cant access any other ROM and my apps wont show any where on phone but are def. on my SD card. PLEASE HELP! i have read other complaints similar but not specific n still havent seen an acceptable answer. Of coarse i can re-DL them but thats not the point and please save ur breath n dont tell me im to clueless to be do n anything root as in a few days i'll be WRITING my own ROMs( of coarse that last part was Bull Sh*t but please help anyway cuz apparently i'm slow) i should state the whole reason i,'m rooting is ultimately to raise the volume on all sounds but mostly on media so i'm also very open to suggestion in this regard. (THANK U in advance n please please feel free to remind me of the thanks button as i dont ever mean to be rude or dismissive)