Have 6 channel amp what's next ?

You should *seriously* consider one of the (soon to be released) UMC-1 pre-processors from Emotiva.com It is a state of the art processor using the latest Cirrus chipset - same chipset that is used by the Cary Cinema 11A ($2500) and the new Krell Pre-pro ($35K - yowza!!).

The UMC-1 will sell for the princely sum of $699 - that is not a typo! This pre-processor has just about every input and output that you could ever need and it will decode all of the latest hi-def codecs. Check out this features list:

Twin Cirrus® 32 bit dual core DSP’s for uncompromised high resolution HD audio decoding

Decoding support for Dolby Digital, Dolby Digital EX, Dolby Digital Plus, Dolby Digital True HD, Dolby PLIIx, DTS, DTSES, DTS HD, DTS Master Audio, DTS Neo 6, SPDIF, PCM 8 channel (note: some audio formats only supported via HDMI)

Genesis® Torino high performance video scaling engine with full Faroujda DCDi® processing
10 bit video resolution
Automatic Emo-Q™ multi channel room correction and automatic loudspeaker setup. Calibrated measurement microphone included.

Quadruple bass manager with independently selectable high and low pass frequencies from 40hz – 160hz

All legacy video inputs can be scaled and output over HDMI at up to 1080p

HDMI sources can be format converted to component video up to 1080i

Full color graphical OSD over live video, including HDMI

All inputs are assignable and feature input labeling, selectable decode modes, selectable triggers, etc.

Independent graphic EQ and bass and treble controls

0.5dB level trims

High voltage, low impedance main analog outputs (7 VRMS)

5 - HDMI inputs and 1 HDMI output.
3- composite video inputs (RCA)
3 - S-video inputs (S-video mini DIN)
3 - component video inputs (RCA)
1 - component video output (RCA)
4 - stereo analog audio inputs (RCA)
1 - 7.1 analog input set (RCA)
1 - 7.1 analog output set (RCA)
4 - coaxial digital inputs, (RCA)
4- optical digital inputs (Toslink)
1- coax digital audio output (RCA)
1- optical digital audio output (Toslink)
1 - Stereo or 2 channel analog multichannel mix down output for fixed level monitoring (RCA)
1- stereo analog variable and independent Zone 2 output (RCA)
1 - stereo analog fixed level record output (RCA)

High performance AM/FM tuner with 24 FM and 6 AM presets
3 - assignable trigger outputs Movie/Music/Amp (3.5mm mini)
1- IR input (3.5mm mini)
1 - IR output (3.5mm mini)
1. Microphone input (3.5mm stereo mini)
1- USB data input (for software upgrades only)

There are some options for you but first things first. You have a 6 channel amp and want 5.1 so assumeing you use a powered sub you will only have 1 extra channel for multi zone use, thats one issue you need to understand.
You could get a another cheap used 2 channel amp so you free up those channels for multi zone on your Pre/Pro, so yes you do want HT Processor, Rotel, Emotiva, Outlaw, and a few others will be in that budget but its gonna be very limited with your desore for HDMI. Emotiva is at some point soon bringing out a Processor that would be perfect for you but its been delayed, you dont need HDMI unless you really want the new HD audio formats that are very limited in release, choosing instead a unit that runs Component (red, green, blue) video may make more sense financially and run seperate digital audio feeding the HDMI direct to monitor for best picture. You dont mention speakers so do you need to buy those and sub or did you just not give that info? If speakers need to be looked into then forget HDMI in you Processor for that amount.
I will PM you if you want to call maybe I can help with some questions. cheers and Happy Thanksgiving

I have an inexpensive 2-ch amp for the 2nd zone and in regard to speakers I have in wall fronts, a B&W Matrix for the center and in ceiling rears already installed and ready to be connected. I have a sunfire powered sub as well. I just figured that for the best Picture/Audio I should use HDMI 1.3.
Is this not correct ?

Yes and no, if the Plasma is 1080p and you intend to watch many Bluray movies then HDMI either into a Processor (like Emotiva mentioned) or you can go straight HDMI from disc player, Satelite and Tivo (make sure you have enough inputs) into Plasma direct then you would go Digital Coax or Toslink wire for audio into the Processor if it doesnt have HDMI, the only thing you will loose is the most advanced HD audio on Bluray discs only as Satelite at this point doesnt support these formats. You can also go multi channel RCA inouts from a Bluray player with a built in decoder and get the HD audio with need for HDMI circuits.
The bottom line is budget, if you cant swing a HDMI processor its not the end of the world and you have options to get around that. I did send a private message if you want some more info.

If you can bi-wire/bi-amp your center channel, that would be awesome. Otherwise, the 6th channel will not be used. Make sure that you don't have a signal into it if it's not hooked up to a speaker.
You will have to get a pre/pro with or without a tuner. If you are new at this, go with a more simple unit if possible. Get a remote that doesn't take a computer tech. I really like sunfire/sherbourne/anthem.
For zone 2: Most pre/pro's will run a second zone. However, using the same unit for this will make things more complicated. Plus, you will need remote IR emitters and such. If you are a novice, either use a completely separate second zone or pay a shop to set it up. I'd suggest selling your second amp and buying a multizone receiver like Denon 385.