I guess it depends on what it is you're trying to achieve.

you say you want it to sound like your old POD X3, but the POD HD has totally different amp models.

let's dial this back a little.  dial in your own tones, and start with just an amp model.  what is the amp in the X3 Pro you're trying to sound like?  it sounds like the MS-Criminal to me (I love that amp model).  on the POD HD try the recto model, and in the DEPs turn sag and hum down to make the amp model more sterile.

Something I've found is that the previous POD amp models weren't very dynamic, and they were very good for metal, because their lack of dynamics sounded like high gain solid state amp models in some cases (i'm talking about the gain models)...  the POD HD amp models are very dynamic (just like the real life things) and not always like the super compressed things you hear on produced CDs, which of course we all try to sound like.  And that's fine, I do that too... but with the POD HD you may need to dial out some of the realism and tweak your tones from scratch to get what it is you're after, and the DEPs can help you there.

basically for me, I never compare presets, as although some of them are great, some of them just don't sound how I personally want my tones to sound.  it's also got to do with your guitar, pickups, style of playing, amplifier or speakers, and the room you're playing in.  and your ears.  everyone is different, and so tweaking tones is sometimes necessary.  start without extra FX, and just look at comparing 2 similar amp models.  get that right and then layer FX on top of it after.  if you stick FX on too soon while you're trying to tweak, it can sometimes become a huge mess and be hard to get it right.

check out the manuals too, if you need help understanding how to tweak your PODs: http://line6.com/support/manuals/

Let us know how you get on

Rowbi