There are a number of factors to consider when purchasing a sub. Below are just a couple.
1) Speaker level outputs are internally amplified at your amplifier’s stage, therefore the signal being fed to your sub is run at a higher voltage. This equates to a greater signal strength, which theoretically provides a cleaner signal over a long run of cable. Generally they are less likely to pick up ground hum (60 Hz / cycles per second), electrical interference, noise, etcetera. However, the quality limitations of your amp are being sent downstream to you sub. Dynamic headroom, total harmonic distortion (THD) and signal-to-noise ratio (S/N level, expressed in dB) can become an issue.
The basic concept behind an amp’s RCA output, is that the source input signal (CD player, tape deck…) is routed directly to a RCA consumer line level connector (usually -10dBV / 0.316 volts), thus bypassing the internal amplification stage. Besides the fact that the quality of the amp can basically be removed from the equation, the biggest advantage to this from of setup is that the speaker level outputs will usually begin clipping considerably sooner than the RCA’s.
Having both types of inputs on your sub will allow you to choose the best option for your particular application.
2) Many subs come with speaker level outputs as well as speaker level and RCA inputs. The capability of your L/R or L/C/R speakers to produce low frequencies / bottom end can be addressed. You can feed the sub's speaker inputs from your amp's speaker outputs and then feed your L/R speakers from the sub's speaker outputs. The internal crossover in the sub rolls off the frequencies below the number you choose on the Hz selector / potentiometer (pot). For example, if you set you sub's pot to 60 Hz, the signal being sent to your L/R speakers does not include any frequencies below 60 Hz (there is a roll off curve, so a small amount does get through, but generally the curve is pretty steep i.e. 18 decibels per octave). This is particularly effective if you are using small L/R bookshelf speakers. They are not being asked to reproduce low frequencies they are physically incapable of.
I realize that ultimately you just want to buy a sub, so I apologize if any of this has caused confusion, but I thought you might find some of the details useful.