New Bass Setup, Help!

[FenderBassMan10]

Hey All, I just bought a new ibanez Sr900 and I need some help setting it up. I've always been a bolt-on neck guy and this is my first neck-through so I don't know how to set it up or anything like that. The problem I'm having is I keep my action very low. This allows me to tap easier with using all 4 fingers on my red hand. The problem is when I keep my action low like this my strings buzz agianst, i believe it is my 2nd fret? Is there any way to stop the buzz without changing the tuning. I tune straight D. If I could tighten the string it would stop the buzz but I dont think theres a way to do that without changing the tuning. Or maybe this is a neck problem that can be fixed?
Thanks for your help!
-Patrick

[BNM]

Did you read the truss rod and action sticky on the top of this board? That may be able to give you a few ideas.