Dual Subs set up advice

Can anyone give me some advice on best practice to run dual subs? I have two Martin Logan Descent i subs for a strictly two channel system with ML Prodigy mains.

My options are:
Speaker level in
RCA in (sub has both left and right in for single sub use)
Balanced XLR (LFE)in (only one XLR in)

I am running the Sonic Frontiers Line 3 which has both balanced and SE outputs.

As of now, I am running them from the 2nd post on my Krell 300M amps but was wondering if it would be just as well to run SE (rca) left out from preamp to left sub in and vice versa for the right. Or, go balanced #2 outs (balanced #1s used for amps) to the single (XLR) LFE in on the subs.

Thoughts opinions?

Run your RCA lines from your preamp as you suggested in option #1.
I"d insert an active x-over in the loop. I use NHT, which is versatile, undetectable (to my ear) in the main path, and relatively inexpensive. This does put another component in the signal path, but (as noted) I find it benign and the seamless hand-off you achieve will be well worth your effort, IME and IMO.

If you really want to see what's possible in this type of set-up, slip an SVS/Audyssey or Velodyne room correcting sub equalizer between the active x-over and the Descents (it will EQ the subs only, and be out of the main path, entirely). I use the Velo SMS-1 (again, relatively inexpensive), but some swear by the SVS unit.

IMO, this was the single biggest audible improvement I have made to my system in the last 20 years.

As always, YMMV, but the SVS, Velo, and NHT units are sold direct with money back in-home terms. If you M does, in fact, V from mine, you can ship it all back at little to no cost.

I use speaker level in on my RELs.
I run RCA out of a SF Line 3 to the two stand alone amp/crossover units for my two Genesis subs. The Genesis subs can be run solo, not dual, so the amp/crossover unit has L and R RCA in. I use the L on one unit and the R on the other.
as you have already tried low level, rca; why not attempt high level speaker level? with my system, speaker level yielded the best integration. in fact, i only use one channel, currently the right speaker level output to feed the one sub i have; would be interested in how two subs would sound.
as you have already tried low level, rca . .

oops, i meant the reverse. but still i find speaker level to be best.
I'm running a pair of ML Descenti's with SoundLab U1-PX's and for me the best feed connection has been to piggy back onto the main speaker terminal posts and feed that back into the RCA in on the sub.
another comment unrelated to the hook up method. Have you ever tried running the subs at different locations? I was at a friends house, he was running ML CLS mains and had two subs. One sub was in one of the front corners of the room. The second sub was placed all the way in the back of the room - middle/center. The depth of the sound stage was amazing. If your cables are long enough, give it a shot and see what you think.
You had better have a large room if you want to try ML Descenti subs in different locations, not to mention moving them around.
I have only one word which can describe moving SoundLabs once they are spiked - HERNIA!
Scousepasty, so to understand you... you feed from the high voltage speaker terminal to the low voltage RCAs on the subs? Or do you mean you run RCAs to the amp and you Y off them to the RCAs on the subs? Or...from the high voltage speakers post you run to the speaker level in on the subs...

At the moment, I run them like the the last option via high voltage but thought it would be just as well to run RCA from the preamp.
I have dual NHT subs, and related NHT SS dual amps. I have three systems, each with separate pre amps. One has dual amps outs, one a sub out, and one with only tape outs. I route all of the outs to a Chase RLC remote controlled unit as a switcher that goes to each of the NHT amps. I do not use the NHT amps to feed the three different sets of speakers that I use individually, all driven by tube amps. Since the line out of each pre amp is different, the Chase unit's remote is used to adjust the output of the NHT sub amps. Works well, gives a lot of flexibility. For WAF purposes, each sub is in a front of the room corner, but I have been testing various other placements. Nothing finalized yet.
I use an Audio Control Richter Scale crossover for a similar setup. It has a built in EQ for the bass level and this helps a lot in balancing the setup. It operates at pre-amp level only however.
Sorry for the confusion NAk, I use a standard speaker cable run between the speaker teminals on the sub to a piggy back RCA's into the main speaker teminal on the speaker. Left sub to left speaker and right sub to right speaker.
It does show how to do this in the ML Descenti manual.
Scousepasty, you have RCA jacks on your speakers? Do you mean you run lines in parallel from your speaker input terminals to the speaker level in on the sub?

The way I am running my cables is essentially the same, in parallel.