That's great news, now you can just do everything through your headunit.
I could go on for days about tuning but to put it simply, there's really not that many choices to choose from on your headunit. When I look at your manual on page 66, it says the HPF is -12 db/octave slope and the sub slope is -18db/oct slope. There are no other choices on slope, but you can choose the frequency cut off though. They are definitely a good start for people getting into this hobby though. You get the most control out of your speakers when you use a Digital Signal Processor (DSP) or a better headunit with active capabilities. I would suggest to keep it simple and work with what you got before you dive into a new can of worms. Work on making your speakers sound the best they can before you even introduce the sub. Are you running stock speakers or going to get new ones? Either way you're gonna have to integrate the speakers and sub to a place where their frequencies meet. Your goal is to not have any huge gaps between the crossovers. I would start with hearing how low your mids can handle without distorting and/or rattling. Hopefully they can handle as low as 80 hz, that way you can just set your sub at 80 as well and call it a day. You can either have the xovers overlapping or underlapping. Up to you. If you feel it's too much or too little in that place, you can always EQ it to your taste.
here's a nice little article on understanding crossovers
Understanding Speaker Crossover Points - AVS | Home Theater Discussions And Reviews