Subwoofer. Great one song. Not so great the next song.

I have found it is a matter of not over-doing it. I am not a fan of ports, especially rear ports, so I advise keeping them stuffed. (my experience below)

Main System, 15" Woofers, Horns, I am familiar with full range and Stereo Bass.
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Both subs and surrounds should not be obvious, (except designed directional action, helicopter fly over, crowd noise ...).

Surrounds: not obvious, but they should surprise you how they were involved when you turn them off, the sound simply collapses to the front.

Subs, location not detectable, their ’fullness’ disappears when off.

1st, successful adjustable crossover
2nd successful adjustable volume.

i.e. Home Theater, Velodyne 10" 1,000 watt self powered sub. Jurassic Park Dinosaur Stomp, oh yeah. But otherwise never muddy.

i.e. Office System, B&W bookshelf speakers and Velodyne 12" self powered sub, doing what the 6-1/2" woofers shouldn't even try do to.
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Consider where eq to separate bass, or separate highs?

Home theater, full frequency to front mains, then:

center to center, surround to surround, sub line out to sub line in, which filters highs,

This keeps full range to your front mains, very important when using ’Direct’ or 2 Channel, you still get the bass to your front mains. Cable ’invents’ strange mixes, I often find 2 channel sounds better.

Office, small 6-1/2" mains: amp speaker wires to sub, sub filters bass out via adjustable crossover, then speaker wires to bookshelf. Then the bookshelf do not try to make bass they cannot do without distortion and poor volume.

Rear Vents Mistake

I inherited a big Fisher Console with horn tweeters, horn mid, and 15" woofers,

So, lets build separate enclosures for them. I duplicated eveything, simply relocated the front panel with drivers, crossovers, insulation into the new enclosures. Wonderful.

Then, being a young whiz kid idiot, I thought, I’ll make larger enclosures, more cubic feet, and a rear vent, get even more out of those monster 37lb woofers.

Engineers at Electrovoice (before mergers ... were still in NYC and Bucanan, Mich), My AV Consultant (I designed a lot of Conference Centers, AV rooms) My Furniture Manufacturer, we all got enthusiastic.

Whoopee, for a while, then sensibly stuffed up the ports.
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Location.

My very heavy mains are on 3 wheels (never wobble, more weight per wheel), and perform pulled out of corners, and away from side walls, toed up slightly. toed in for wide enough center imaging for two listeners. They roll into the corners when I expand the dining room table for holidays.

I mention it, because, if the front mains are heavy enough, that can solve situations like you mentioned, limited choices of location. Solid, spikes, 3 wheels, I’ve done them all.

One possibility is that, because you haven’t done any PEQ, some frequencies are being reproduced at the (mostly) correct SPL while others are too loud and overwhelming. The e110 doesn’t have any PEQ functionality built-in so you’d need to add an outboard PEQ device.

Good advice.

Also, in order to optimize the subwoofer integration, you should be connecting your pre-amp to the e110 inputs, and the e110 outputs to your speaker amp, which is then connected to the speakers. This ensures the e110’s crossover is applied.

There is no crossover in the e110, so there's really no point to doing this.

Turn the FEQ, all the way down, Counter Clock Wise.

What's an FEQ?

My suggestions are to consider a preamp with bass management, an external crossover and/or an external DSP for equalizing the sub in your room.

Plugging ports on a speaker isn't the same as the speaker having been designed with a sealed cabinet to begin with. So instead of plugging the ports, it would be better to set the crossover high enough that the speaker ports are unused (or mostly unused) while leaving them unplugged.

Read Jonathan Valin’s review of this sub in the June, 2014 Absolute Sound...very educational. Actually, read all of the reviews on this sub, which will help in set up ( a 2nd unit would be beneficial ), but I understand the room use situation.

In my opinion there's no doubt you should hear a worthwhile improvement by using some of the suggestions given here along with a little effort despite your restrictions.

+1 oldhvy's is free.

Your little JL may lack EQ but its a quality product that will provide you service regardless of any down the road room or system changes. Its also worthy of the benefits of equalization in your future. 

Keep at it and have fun with it.