Why use samples if you've got a turntable and mixer? I'm pretty bad at scratching, but it still sounds better than some sampled sh*t.
I don't know if you record your scratches on a multitracker or sample them in your MPC, but there's ways to make them sit in your mix both ways.
First try adjusting the the eq on your dj-mixer. You could also try and add a little ghetto distortion by increasing the gain on you mixer untill it starts to clip pretty bad (turn down the input-level on your MPC to compensate).
If you're recording on a multitracker or something like that, use a compressor.
If you're sampling into the mpc, try everything

Downsampling, lowering the samplerate to 33Khz. Filtering etc.