Two subs in two boxes?

If I understand your question correctly, you have one sub now, but you're thinking about adding another one in a separate box...and you want to know if the quality of sound will be as good?  If I have this right, the answer is the quality of sound will always change when you change the number of drivers on an amplifier.  It could be a change for the better or it could be a change for the worse.  Reasons are, the impedance will change and the amplifier will work differently, either harder or easier.  For example, if you have one 4 ohm sub now connected to a mono amp, the amp will output at 4 ohms.  If you add another sub to it, the amp will either output at 2 ohms or 8 ohms, depending on how you connect the subs.  The amp's power output will work best with either one way or the other.  And that depends on what RMS power rating the subs are and how much power the amp outputs at the different impedance loads.

Provide more detailed info if you have more questions about this.  Like what kind of amp is it...mono or two channel...provide links if you can or model numbers of amp and subs.

It's hard trading up amps.  You have to find a buyer for one and also have the replacement in place before you sell it.  There's almost always money lost.  Consider these things:  You will always want subwoofers from this point on, at the point you have it up and running, that is.  Whether you like that particular sub or not will depend entirely on the complete installation, including the two most important things:  the enclosure and the sound damping in the vehicle.

Now, given the above....you should consider making one amp purchase for the sub or possibly two subs.  Make it a mono amp capable of powering one sub at 4 ohms or 2 subs at (total) 2 ohms.  Buy the single 4 ohm sub and hook it up.  Build the box so that it specs out correctly for that sub.  The amp should be rated (I didn't look these particular models up but it looks like you know what to look for) at enough power at a 4 ohm output to power the sub.  That power should be 50% up to 100% of the RMS rating of the sub.

If you like the sound and it's loud enough, stay put.  If you don't like the sound, consider shopping for a different 4 ohm or DVC 2 ohm sub that will work in that enclosure.  If you like it but you want louder sub bass, get a second sub, build a second identical box and connect them each to the amp.  The subs will be connected in parallel.  The amp will still output enough power for both subs because now it will be providing power at its 2 ohm rating.

I looked at the JBL products you mentioned.  The sub is RMS 250 watts.  The 301 is too little power and the 601 is too much power for what you have in mind.  This MTX amp is not of the quality of the JBL amps, but look at it's power output ratings, which are correct for the sub(s) you have in mind.

I used the 50% and up to 100% as a general rule when selecting amp power, but you'll find that using 50% is generally done (if at all) for the main speakers in a SQ setup but not generally for subs.  Most people will try to power at 100% of sub RMS.  I thought the 301 might be a little shy of power in a two-sub setup....but I'm not real familiar with this amp and I could be wrong.  It would certainly drive the two speakers, but going from one to two subs, you may not get the increase in decibels you're looking for.  But if that line of amps is available to you where you're at, use the 301.

As far as regulating power output, it's very tricky and hard to limit the amount of power an amp produces.  But a lot of people, esp. competitors, do it.  If you're thinking of using the 601 that will be the case.  Overpowering a sub will destroy it.  Underpowering, you can play that sub all day long. 

Just don't ever feel the desire to turn the amp gain once you have it set to match the output of the deck.  Once set, it should not change if there are no other signal processing devices placed in the signal path.  You should set it with the first sub install, and then again using the same methodology when the second is installed, because the amp will be outputting into a lower load.  It may not change the position of the gain, but you would double check it anyway.

The tendency is for one to mess with the amp gain setting when the second sub is installed because of the desire to hear sounds that are much louder.  But the decibel level in this scenario would be an increase of only about 4 db (3 db with the doubling of the speaker cone area and 1 db for the additional power) with the addition of the second sub....just a little louder.

You're probably on the right track as you are now.  The general rule is:  double the power for +3 db;  double the cone area for +3 db.  You will get double the cone area with the addition of any sub, the rest is an estimate of the percentage of power increase.  But I say you look to be on the right track here because that GT120 boasts a 93 db sensitivity, and the type (IIRC in the owner's manual) emphasizes this efficiency by stating that it works well with less power.  If you compare its output to a sub with a 90 db sensitiviy, it will play as loud with half the power as the other sub.

Efficiency ratings can be skewed, though.  I noticed recently that Infinity is rating "in car" efficiency, which leaves you little for comparison.  If you have any access at all to setups with the different budget model subs, have a few listening sessions before you decide.  I don't have a recommendation of one over the other, just because I haven't evaluated them.