This is my first arduino board. I want to just use ISP for uploading for now, later will use ft232r chip. I have a mini-usb there just for the power. is there problem with my npn configuration ? I copy that from another circuit.
also, is it a good idea to add resistors and LEDs to my digital pin headers pin8-pin13? pin13 already has one led. will adding LEDs disable the function of those pins?
If you plan to use serial for upload later, you should make a header for an FTDI adapter (the 6-pins in a line with RX, TX, Vcc, Gnd, and DTR, DTR connected to one side of 0.1uf cap, other side of cap connected to reset, and reset needs a diode to Vcc (so that reset line can't go above Vcc, which has sometimes bricked chips by briefly entering HVSP mode when DTR is released).
Don't use an NPN transistor in an emitter follower configuration unless you have a good reason for doing so. The internet is full of people throwing around emitter follower circuits as if they're a good "default" way to switch things with NPN BJT transistors (much worse, people just 1:1 swap the BJT with a MOSFET and post that as viable designs - clearly without having actually tested their own design ;-) )
What you want to do is connect emitter to ground (not + side of load), connect + side of load to the supply voltage, and - side of load to the collector of the transistor, base to R5.
Or use a MOSFET - Source to ground, emitter to - side of load. Gate goes to the IO pin, with a 10k resistor between gate and ground. Optionally, put a small (100 ohm) resistor between gate and IO pin as well (some people get worked up about the very brief pulse of current down the IO line to (dis)charge the gate capacitor, which could for a split second exceed the chip's current rating, and put a little resistor in there - I've never put a resistor in series with my mosfet gates, though, and my stuff works. So take that as you will )
No need for extra LEDs and resistors on those pins, unless you need them for something. When I put LEDs on data lines (which I do only when I need to - say, to visualize when the line is in use), I use 1k-2k resistors - they're still bright enough to see for debug, while having less impact on the voltage while the pin is high. Usually the LEDs won't cause problems, but i err on the side of caution, and use large series resistors.