Need Suggestions/help

[LexBaller]

hey im new here and i have a 99 es300 and the system is stock right now. i have either a alpine 9815 or 9835 i forget which 1 thats not hooked up. i need 2 get the factory amp bypassed cuz im gettin a kicker L5 12" to put in the trunk and a new amp for that. so my question is A. will the stock speakers sound better hooked up to the alpine and B. how much is a shop gonna charge to bypass the factory amp and install all that because it sounds like its hard to install systems on lex's. any help would be appreciated thanks!