This has been discussed, at least in part, previously. It's really not clear what your problem is.

ISP is the vehicle you want for programming your MCU in-situ, meaning after it is soldered into its circuit board.

I'd caution you that there has been very much discussion about ATMEL MCU's and their programming circuits. If you have taken any "liberties," meaning that if you have substituted any components for others not in the application circuit that the mfg has published, it is likely it will fail.

You must build EXACTLY the circuit published, and use it with EXACTLY the MCU for which it is designed, omitting nothing and adding nothing, if you expect an ATMEL circuit to work. That means that if it says 22 pf or 1100 ohms and you use 21 pf or 1000, ohms, you are likely to fail.

You should pay particularl attention to the reset circuitry and the extensive discussion of it.

RE