Direct By- Pass

I am wondering if there is a difference between A Direct
analog signal on a pre-pro vs using the analog inputs.
I hope I stated this correctly. I see many comments on
people getting a Pre-amp with a HT passthrough and I'm
a little confused on how pre=pros do analog 2 ch.

There is a difference, most pre-pros will take the analog 2ch source like a cd player, send it through its digital processors, then to it's preamp section, even when you use the RCA style input. The music is getting converted twice, once from your cd player or dac and then through the preamps A/D chips. Unless it says true analog by-pass this is whats occuring.
Receivers without a pass through get digitized by the DAC and degrade the sound. Receivers with the pass thru keep the signal analog using the CDplayers dacs.
I think I'm following this - So if a pre-pro does not have A
HT pass or direct pass, the sound can be no better than the
pre-pro regarless of whether I use the digital cable to the pre-pro or the analog RCA. I have read on this site some
things on HT pass and this helps clear this up.

Finally is it better to have a HT pass or direct pass? If
it's a direct pass than is the sound still from the pre-pro
just using the dacs from a CD player?

Direct by pass refers to bypassing the digital section of a HT pre/pro, it's a feature of the multichannel processer. HT bypass is found on a integrated amp and allows a HT pre/pro to bypass the integrateds pre section, to use it like a 2ch amp when watching movies. Then you can use the integrated amp normally while listening to 2ch sources like cd, without having to disconnect a bunch of wires to watch a movie.