big newbie here seeking advice

You effectively bought a 3.1 set up and u have a CD player - u need an amp/AVR to power those 3 speakers

You're going to want a 5.1 or 7.1 channel receiver and some surround speakers to complement the fronts and center; you've got the 3.1 for sure, just 2 speakers short (or 4 if you want crazy 7.1 woooo).  You want to use the digital out of the SACD to the zero for just the headphone setup, then most likely the 5.1 analog outputs of the SACD with regular RCA analog cables into the 5.1 or 7.1 input (a bunch of rca jacks basically) of an audio video receiver.  The other option is to get a regular integrated amplifier (stereo amp with volume knob on the front) and a regular RCA cable to just do stereo audio with your front speakers, connected to the SACD; as for the sub, you can pass the speaker cables through the sub's speaker passthrough to give it the signal, or something like that.  You can also feed it a stereo RCA signal from the cd player and then set the filters etc etc so that its bass doesn't kick in at too high of a frequency, such that it complements the front speakers.  

I have a Marantz and I like it fine.  I don't feel like I'm in any position to evaluate home theater gear, because I won't have a really good home theater setup for a long time (room wise), and I'm using to listening to high end balanced headphones, to where no receivers & speakers are going to entertain me much.  My favorite speakers are my car stereo...

I have an older yamaha htr-5890, I've seen them go for about $250- on amazon. It's 140wats per channel and seems to be one of the last models with a phono jack. It seems to be good at everything, i.e., powering big speakers, surround sound, tuner, etc. I dare someone to find a better deal at $250-.   

Actually just for music stereo 2.0 floor standers or 2.1 bookshelf + sub would suffice but are you looking to build up a HT for example? You mentioned only being able to use that CD player