(No offence here!) It sounds like the active sub you have may be cheapy and probably wasn't designed to offer a huge amount of bass. Generally, active subs are pretty terrible anyway. What head unit did you upgrade to? If it's a low end chinese head-unit, you'll notice the difference in quality and you won't have as many settings to play about with in order to get the best sound out of your speakers and subwoofer.
As far as the upgrade of speakers, the standard speakers aren't THAT bad - when I say this, I'm comparing them to a set of £30 JVC replacements. You may notice you won't hear much difference in quality, or you may even notice you've lost a bit of low end frequency due to the JVC's not being able to put out certain lower frequencies. Ask yourself - are the JVC's really an 'upgrade'?
I have a single 12" Pioneer competition subwoofer with dual 4ohm voice coil, rated up to 800watts RMS but people have passed nearly 1Kw through these subs before. This is powered by a JL Audio JX1000/D amplifier. It certainly pumps out some bass and at some superior frequencies too, box being built to suit frequencies best at around 33-35Hz. I haven't changed any other speakers because the factory ones are more than capable of handling high volumes if you have a head unit that is able to tune out a lot of lower frequencies. I have my front and rear speakers set to HPF (High-Pass Filter) ~80-100Hz. This means at high volume, the speakers do not distort. The bass comes from the 12" sub in the rear and the speakers take care of the mids/highs. I have contemplated upgrading the speakers to some Focals but I gave up because I don't play music often, and if I do, it's always on low because I genuinely enjoy the sound of the car than any music that is playing haha.
I would check your head unit settings and pre-outs on the head unit. If you have a dedicated Sub output, you may have some options here to increase the volume a bit, if that is what you're after. It may be that your active sub requires a certain voltage from the pre-outs on your head unit but without knowing exactly what kit you're dealing with, it's difficult to tell.
Drop me a message if you want some more help with the sound system!