OK. If I understood your problem, you want to overwrite CC messages on a MIDI part just like you would overwrite automation events with your controller. If this is the case, I'm afraid it's impossible, because MIDI part recording just records MIDI messages while automation handling has some intelligence built into it.
Cubase4/SX1/VST3.7 | Waves Gold | Melodyne | PC Core2Quad/4G/2xSSD/WinXP32 | MacMini | Frontier Tranzport
Tascam DM-4800 | Soundcraft Spirit Studio 16 | dbx231 | Genelec 1032A | KEF C15 | Auratone 5S | Samson S-phone
Yamaha REV500/SPX990 | Alesis Midiverb4 | Roland SDE-330 | Pearl Echo Orbit | Aphex 109 x2 | TL-Audio C5021
Alesis 3630 | AudioLogic MT66 | Joemeek VC1Q | dbx386 | Focusrite VoiceMaster | Line6 PodXt/BassPodXt | Boss GT-3
Roland TD8/TD5/JV2080/SC55 | UseAudio Plugiator | E-mu ProteusXR | Akai S-900/AX73 | M-Audio Keystation
Martin/ESP/Fender/Line6 guitars/basses | Pearl drumkit | Olympic by Premier drumkit | Custom Roland V-drum kit
Neumann M147 | Earthworks QTC30 | RØDE NT2/NT55 | Shure SM57/SM58/B57/B58 | Sennheiser e606 | AKG D112 ...
... Saeco Odea Giro Espresso machine | BMW Z3 roadster | American Pit Bull Terrier