One sensor produces a sinewave that does not go much above 50mV, at around 5-8kHz. The other produces a sinewave...
The Arduino cannot accept or read the negative half of an AC waveform. The Arduino can be damaged by negative voltages and if the Arduino survives, the negative half of the signal will be clipped-off. (Minus 50mV won't hurt the Arduino, but you'd only be able to read the positive half of the waveform.)
The simplest way to handle the an AC waveform is to [u]bias the input[/u]. With the input biased at 2.5V, you'll get an ADC reading of (about) 512 with no signal. You can subtract that out in software if necessary.
You won't get much resolution at 50mV.... You should be able to "detect" the signal, but with the 10-bit ADC and the default 5V reference, you get a resolution of about 5mV per count. i.e. If no signal reads 512, 50mV will read 522 (on the positive peaks). You can use the optional 1.1V reference for about 5 times the resolution, but you'll have to lower the bias voltage.
Need some advice/help here...I have a standard sine wave analog signal that I need to split into two signals...
Since the Arduino has almost infinite impedance you could probably connect one signal to 100 Arduino inputs!!! (There is some capacitance, but at 8kHz or less, that shouldn't be an issue.)
There's a general rule that you can connect multiple inputs together, but you cannot connect outputs together.
It doesn't really matter how I get there, as long as it's reproduced into to separate signals.
It's not clear what you mean by "separate".
...but are there output pins assignable to replicate it?
No... The standard Arduino doesn't have an analog output. (It has PWM which can dim an LED or otherwise sometimes approximate analog.)