Hi. I know this is kind off topic, but I'm not active in many forums so I'll try a shot here.
I have an acoustic amp with two channels inputs , and sometimes I'm in need to use three channels, two mics and one guitar.

I also have a little two channel mixer that I want to use the two mics on, combine them into one input on my amp, and then use the second one for my guitar. Is this possible in some way? I was thinking about using two split mono jacks from the mixer into one stereo jack on the amp, but since the inputs are mono I don't know if it will work.

Does anyone have any ideas here?
The amp is a fishman loudbox and the mixer is a yamaha mg06x

Two inputs on amp.  Run guitar to one input.  Run both mic's to the mixer and output of mixer (either channel if the mixer has two channel output since its mono) to the second amp input.  You can control each mic's volume level in the mixer.

As Jack said, pretty straight forward. 
Even if the mixer has stereo out that doesn't matter, just use the left or the right and make sure the PAN is in the center for the mike channels. 
 
A few things are a matter of what the amp has for input jacks and what the mixer has for output sends. 
 
If you post the make and  model of the amp and mixer we can give you exact instructions on how to hook it up. 

Pretty straight-forward, and the idea presented is the best way to do it.
 
There are a couple caveats:
 
Your mixer has an odd input architecture - you must put channels 1 & 2 into mono mode to get both of them sent to both outputs.
 
You will need to connect one of the outputs to one of the inputs on your amplifier, but keep in mind that the signal is line level, so you'll need to turn down the input level for that channel on the amplifier.
 
Probably best to use an XLR to XLR cable to connect the mixer to the amplifier.
 
Other than that you should be good to go.

And do not be tempted to try using a "Y" cable for the microphones. I'm too lazy to type out the explanation, especially when Dennis Bohn did so brilliantly HERE. Probably the single biggest mistake I see out there in the real world.

Well 5 days and the OP has not returned, but I was thinking if it were me I would use the mixer for everything  so I could control my mix from a side table. Not sure which Loudbox they have but the mini only has one XLR so it's as simple as that. All you need is one regular mike cable to run from the mixer to the XLR input of the amp. 
Guitar and mikes into the mixer where you can even use it's effects if so be it. You could even have a second guitar ready to go.