Hmmm....is it just me?
OK, you want an EXACT answer to a very vague question while you provide no real information except "big sub", "little sub" and "audiophile". Granted, you are a noob but as with everything, garbage in = garbage out and it is hard to dig up good information out of the garbage can of information you provided. Now that is an EXACT answer!
Most noobs list their subwoofers assuming everyone on AVS forum as a working knowledge of every subwoofer manufactured in the past 30 years--they assume wrong. Or, for some unknown reason the forum members are supposed to look up whatever subwoofers they use then spend our time figuring out what is wrong. If they don't do that, the OP gets butt hurt so we live in fear of not being "nice"? Really?
OK, this is what you SHOULD post. I have Subwoofer X which is a sealed/ported/bandpass/infinite baffle/horn loaded sub with this size driver(s) inside. I am attempting to mix it with Brand Y subwoofer which is sealed/ported/bandpass/infinite baffle/horn loaded sub with this size driver(s) If they are ported/bandpass, they are tune to a frequency of X Hz. The size of my room is X cubic feet/cubic meters and I listen at XXX dB. My main speakers are Brand X and sealed/ported/infinite baffle/in-wall or mounted in the ceiling.
What is a "big sub"? To me, it is a subwoofer that uses an 18" diameter driver or multiple smaller drivers that move several liters of air and can produce over 115dB of output at 20Hz. A "small sub" can't be defined, it can be a Bose bass box, a 6 inch driver used for computer desks or an 8 incher in a sealed box. Subwoofer drivers range from 6.5 inches (Tang Band for instance) all the way up to 40 inch PowerSoft stadium subs or a 50 incher or 80 incher from a manufacturer in China--they do exist.
To get the best sound quality out of subwoofers, it is best to use 2 or more of them--they should be the same alignment (sealed/ported/bandpass etc.) and when tuned, they should be tuned to approximately the same frequency or within a 1/4th octave of each other. If you mix sealed/ported/bandpass/horn loaded/infinite baffle together--you WILL have problems! There are ways around that but it requires one to get deep into the weeds, take a large amounts of measurements and processing and so on for success. That is not something a person that does not fully understand the physics should attempt--rolling the dice and keep screwing around with mixing different alignments of subs together does not favor chance.
Very easy to spot you attempting to take a ride on the fail whale. You are mixing two different subs together (alignment not specified) you are running each one on it's own (best to use more than one sub for best sound quality) but you did notice "smaller" subs are easier to setup. Want to know why? Simple! Generally speaking, smaller subs don't give you the extension of larger subs. They don't go as low with any meaningful SPL. The lower in frequency the subwoofer provides, the more standing waves, peaks and dips show up in the response because the wavelengths get much longer and as that happens--you create more problems. If you have a small "sub"
that cuts off below 40 Hz then you have a big sub that gives solid response down to 16Hz--you just created acoustic chaos with the response unless your subwoofer is either outside or you live in a sports stadium so the 70 foot wavelengths don't fold over, create peaks/nulls etc. Very simple to screw around with 40Hz capability, very little skill required but once you want 16Hz or lower--then this becomes much more complex, much larger subwoofers, multiple subwoofers and so on.
For instance, my garage is not very kind to acoustics--it's a garage. Did some testing and I get some nasty stuff in the low 20Hz range, huge peaks/nulls and a standing wave that beats my garage door to death as it hammers away on the hinges. I built a dual 15" sub, tuned it to 24Hz and threw a high pass filter at 21Hz while undersizing the box to create a roll off at around 27Hz. That eliminated most of the problem by avoiding that peak acoustically and I can always open the garage door to change the "room acoustics" if you will. I designed to run the sub both sealed or ported so if I have to blast the system with the garage door closed, running sealed prevents high SPL response down low which prevents that standing wave. You design the system around the flaws in the location, heck...I had to build line arrays to prevent floor/ceiling bounce but that is the extreme. It does work very well for a garage--but way off the beaten path and a pain in my butt.
Some advice when posting, give all the information you have on your subs/mains and room used. Give us a clue of what you are using the system for, music, movies, gaming or whatever. Throw in a rough guess on what sound levels you expect to use and an idea of how low you prefer the subwoofers to play. Don't use vague, meaningless terms like "big", "small" or audiophile...we need real terminology because test gear, measurements, test results on speakers, amps or whatever don't contain marketing terms.
Final answer? You are doing it wrong--not the answer you want to hear. That's OK, all part of the learning process. Have no idea if you can mix those two subs because it is just a piece of the puzzle and the answer depends on many other factors that are unknown. If you want to know if you can use your existing system together or, how to get it to work better--that demands more information. The only exact answer I can provide is you are doing it wrong, if you want to get better results we need much more information which only you can provide. Some people like to throw money at a problem and hope that eventually by random luck they can get the sound they want. This is fine as long as wasting time, effort and money is OK with you--for some people that is the entertaining part of the hobby. However, most people on this forum don't want to waste time posting multiple answers over a period of days/weeks/months as most people tend to not have the time to follow the thread.
Good luck with your quest, hopefully some day the audio gods will smile upon you before you run out of time, money or sanity.