One thing that hasn't been pointed out is that the Z87I in the 250D is a bit awkward. Most of the connectors sit along the top edge of the motherboard, which is right next to the two 120mm fan locations. This means that however well you tie up cables, you'll have a lot of mess in this area, seriously impacting the need for these fans, as well as making the use of splitters increasingly complicated (routing the cables will be an issue).
Generally, two system fans is probably sufficient for an ITX system, and it's usually fairly easy to run a single splitter from the system fan header, so you control these fans together. This works best if the fans are similar/identical, but it's fairly solid regardless. If you have three system fans, then you can attempt to run them from the same header, but you'll start to run into issues with having enough wattage (this depends on the motherboard and the fans).
It is possible to run a splitter from each of the fan headers (CPU and System) so one of your fans is controlled off the CPU temps, but it's not ideal, and again, will depend hugely on what CPU cooler you are using, and the motherboard.
If you aren't using the ODD bay, you can purchase a fan controller. These don't need to be expensive, and you can run a near infinite number of fans from these. If the ODD is in use, then it might be possible to fit a smaller fan controller designed to fit in a 3.5" bay, either in an available drive bay, or attached to the inside of the case with an adhesive pad. It'd not a good solution, as it's messy and you wouldn't be able to control the fans on the fly, but it would give you the ability to find a healthy balance of noise/performance.