Whether you'll get better sound these days out of tubes is debatable.  I know it's the standard line, heck, I spouted that line myself for many years. But I've always been one to not drink the cool-aid and think and listen for myself, and I just don't think that's true anymore. I've played guitar for 40 years now and most of that time has been through tube amps.  But the fact is devices like the HD500 and other high quality modellers sound good through FRFR systems. I thought the Bose L1 was the best sounding rig when I had my DH500 in front of it.  In fact I preferred it to the sound of my Mesa Boogie Mark V.  But I recently sold my Bose L1's and bought 2 L3t's one L3s and the M20d mixer.  With or without the mixer the L3t gives an even better guitar tone than the Bose did.  And to add to the fact that guitar modellers have gotten really good FINALLY!!!, you also have to consider that if you give the exact same guitar rigs to 10 different players you'll have 10 different guitar tones, so to tell someone they'll get better sound via tubes IMO is a maybe at best.  The fact is, you can get awesome guitar tones out of an HD500 L3t setup.  In fact I would bet comparable to going through an HD. If you have an acoustic or a Variax then hands down you will get a far better acoustic sound going through the L3t. 

L6 Link works, and so do the HD500 analog outputs into the rear panel line inputs on the L3t. I have tried/used both. I found a significant volume difference; the L6 Link seemed much louder though I confess I did not spend any time playing with the L6 Link settings in the HD500.

In terms of acoustic versatility I found I got the best results by using the HD500 analog outputs for electric guitar, and plugging an acoustic guitar directly into the L3t mixer (Channel 1) and using the Acoustic feature on that channel. I find I can get a better acoustic guitar tone that way vs. using the HD500 for an acoustic preset. Again - this was my finding based on limited time invested. It was easier to balance the volumes between the acoustic guitar and the HD500 using the HD500 analog outputs in conjunction with the L3t mixer.

I believe that with more time I could probably find a good way to use L6 Link with the HD500 and maybe set up an acoustic guitar preset that uses my JTV-59 thru the HD500 to obtain a better tone than my acoustic direct to the L3t mixer. I think I could also use the HD500 L6 Link settings to customize my presets for electric vs. acoustic guitar output...... but I haven't done any of that (yet?).

Bottom line: there is probably no 'best' way to hook up the HD500, L3t, and an electric/acoustic guitar mix. There are several ways - what matters is what works best for you, and that will take time and experimenting.