Atoms are fantastic! Though I think they've been around a long time! Anyway, the nice thing about your LPA-1 is that it never goes obsolete. I would just stick the pre-outs from your receiver on to the LPA-1 like they've been labelled using RCA cables and match it to the corresponding speaker.
Leave the ceiling speakers for your receiever to power.
Transport: Sony BDP 5100 Blu ray player spdif PC using Musiland Digital Times WASAPI via BNC connection - DAC: DC-1->XLR XPA-1 , RCA->Basx A-100 CD: Denon DCD 600 PCM 61 DAC. RCA Amp: XPA-1 gen 2 using XLR connections. Speakers: Axiom Audio m80 V3, Sennheisser HD700 headphones. two pairs 12 guage each bi-wire speaker cables per monoblock Headphone amp: Basx A-100 (INCREDIBLE VALUE!!)
Other equipment: Asus Xonar essence ST Behringer UCA 202 Sennheiser HD600
Generally your big companies like Denon, Marantz and Onkyo jump on the new technologies very quickly. Its been awhile since I looked at their offerings, but previously you had to be at about $1,000 to $1,500 before you got pre-outs on all channels. They churn out new models every year so you can get discounted product at the end of every cycle. The next tier up would be Integra ( fancy Onkyo) and Anthem.