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I'm looking at some speakers for my car. The ones that will be in front have an RMS rating of 50 at 4 Ohms, while the rear ones have an RMS rating of 90 at 4 Ohms. Would a 4 channel amp suffice and if so, what RMS rating should I shoot for? Or would two 2 channel amps perform better?

Edit: my head unit has an RMS rating of 4x16 watts, if it matters.

 
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A 4 channel amp is for running 4 speakers so if you want to run 2 in the front and 2 in the back then you need a 4 channel. You want an amp that is going to provide the closest to the RMS rating. Your headunit will under power the 50w speakers which is just has bad as over powering them. If your going get more powerful door speakers then you should run them off a 4 channel amp.

 
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RMS ratings are also, as a general rule, rated lower then what they can actually handle. You can go slightly above the RMS rating and be ok.

Like ^^ stated, a four channel is what you're looking for. Alpine makes some of the best four channel amps on the market and they will all fall under the power ranges you're looking for. You could technically wire up 2 2 channel amps but that would be a wiring nightmare, and wouldn't give you much different results.

Also know that those power ratings are at 4 ohms. Generally speaking, speakers also have a 2 ohm rating which can handle higher RMS. Check the speaker specifications to see if there is a 2 ohm setting. If so, then you have a wider range of power to work with. Most 4 channel amps fall under 100 RMS per channel, though.

 
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I understand all this, my issue is that my front speakers' RMS is 40 watts lower than my rear. Do i need something close to a 70-ish, or will 100 not kill these 50's?

Or is my thinking wrong and the channels on an amp are adjustable? I've never dealt with an amp before so Im still a newb, lol.

 
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Your right they are not adjustable. The 100 will not kill the 50w. 50W is peak power which is really loud so you will most likely not max them out. An amp in the middle would be best.

 
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Since your front speakers are 40 watts rms, and your rear are 90 rms, You have to go with a lower rated amp (for 40 watts rms). A 4 channel, 40 watt @ 4 ohm amp will definitely work, and your rear speakers will sound fine, but just know your rear speakers can handle more. DO NOT go past 40 watts rms @ 4 ohms. Do not get an amp that's running 40 watts @ 2 ohms either, as this will not work. Yes, speakers can handle slightly more than rms values (RMS values are an average, and are always rounded down). But, even a slight increase to 50 watts rms would still run the risk of blowing the speakers.

Your other option is to wire two amps, each one being 2 channels. One will power your front speakers at 40 watts rms, while the other powers your back at 90 watts rms. It will be a pain to wire. I don't know if it will affect the electrical capability of your car, since you are running two amps. Unless you have a good alternator and battery. If you plan on adding an amp for a subwoofer, look into a performance battery for car audio.

edit:

Just because speakers have both an RMS (average) and a max wattage value, doesn't mean you should power them somewhere in between. For example, if a speaker can handle 40 rms and 100 max at 4 ohms, it's not advisable to run the speaker 'in the middle' at 70 watts. It will blow the speaker after a bit of use. I would advise not even going up to 50 watts rms for the speakers. RMS means a level of power the speaker can handle regularly, while max means it can handle a larger surge, that doesn't mean you run the speaker regularly at a higher level. Stick to RMS ratings, they're provided by the manufacturer for a reason.