I will add:
I thought reference level was when the speakers are loud enough to be studio monitors, provide accurate sound.
Reference is about accurate sound, period. How loud you need it to be depends on your needs, which in turn can also depend on other factors: noise floor, preference, etc. Regardless, the important thing for "reference sound" in terms of the amplifier is very low levels of distortion. Anything after that depends on what the speaker needs: how much power does it need (and how much can the amp give without distortion), does the speaker need a lot of current (ie whether its impedance swings far from the nominal rating - ergo to match it when it dips to 4ohm the amp preferably doubles the power), or does it need a lot of voltage (not as prevalent with speakers as with high impedance headphones - no dynamic driver speakers need that much, and some hybrid designs don't need a lot for the non-dynamic tweeters). The need for monstrous amplifiers only exists because the perfect transducer that has a perfectly flat, fullrange response and flat impedance curve, and has very high efficiency, does not exist yet.
As a personal preference I would always hedge my bets on an amp that generally should make at least 50% more power at 4ohms, although it would be better if it can double the output. My NAD 304 is only rated for 35wpc but stomped on a number of entry level receivers - enough that when a friend did an HT set-up for concerts and will also be his only audio set-up as well (apart from his car's), I brought my NAD 304 when he looked for a receiver to use as a reference. This was circa 2009, with 2008 and prior receivers, so I wouldn't know if the newer ones are still the same, but a lot of the ones below $1,000 tended to sound very different on a lot of speakers compared to the NAD (either warmer or thinner), and some either had too loud bass or barely there (while the 304 had multi-driver B&W towers pounding clean and tight, and much louder too).
Another problem with HT receivers in general is that sometimes they're only tested with one channel running, so they can quote somewhere that "oh it makes 165watts!" which you'd think was entirely accurate if you don't pay attention to "one channel driven, 2khz." Then buried somewhere else in the manual (so it wouldn't be taken that they totally lied, like including the prior disclaimer) it will say, "45w x 5, 2khz, all channels driven."
Given that's a Marantz though I wouldn't worry about it - just hook it up and enjoy the music. However...
I am using an external pre amp found in an apogee ensemble for the digital signal, I am converting its TRS outputs into RCA inputs for the reciever.
...this seems like a roundabout way of handling the signal. Unless I'm using the receiver's DAC, I'd rather use a 2ch integrated amplifier. Still, you already have it, might as well just use it (but of course consider trading it in if you can find, say, a 2ch integrated amplifier).
I asked and was told to have 20W over power for what my speakers handle wasn't dangerous if I was blasting it. So if I kept the reciever around 90. Is this true? I would like to take care of my speakers.
That doesn't really matter - what matters is whether the speakers are clipping. If you have a quiet enough room and a 15wpc amplifier can get a speaker loud enough without clipping, then you can use that. I have a pair of 25w tweeters in my car getting 75wpc from my amplifier, but the gain structure has -6db on the receiver's output and the amplifier's gain setting (not the same as a potentiometer, which is more prone channel imbalance) close to zero; also, the 150wpc channels on the same amp is powering 70watt midwoofers in my doors, with gain at 11:00 and 0 on the receiver. I'd be deaf before I hit clipping and I listen just loud enough to get past the noise that I can't keep out of the car - no parking with doors open and having a concert in a parking lot until cops tell me to hit the road.
Gain would be different so we'd have no idea how loud 90 is - you'll have to be the one to watch out for clipping and distortion. If for example on bass or percussion you hear a "thwack!" in the background, that means the speakers are hitting their excursion limit, so definitely turn that thing down.
So actually a real reference system would have more to do with sealing up a room from outside noise, then getting a neutral enough speaker, then depending on the speaker that you were able to fit in that room, match it with the kind of amp that can drive it properly.