Will a GeForce GTX 980 fit inside an ATX Mid-Tower Case?

Yes, it will fit in an ATX Mid-Tower.

As for your other question about motherboards, the main difference between the $50 and $400 is the amount of features offered by the motherboard. The most expensive motherboards will be the most stable and support the highest speeds & numbers of components.

Additionally, you need to ensure that the motherboard you purchase is compatible with your CPU. Match the socket of the CPU with the socket of the motherboard (e.g. an i5-4590K will go in socket LGA 1150)

Or if you want to skip all the reading, you could also provide a budget and some kind soul could give you a build too

Very large and very small form factor builds brings lots of additional complications into play that should be avoided for your first build. Stick with either a microATX in a microATX mid tower, or ATX in an ATX mid tower for your first build to minimize complications.

Very cheap, and very expensive motherboards should also typically be avoided for your first build. $50 motherboards are typically built to bare minimum standards and aren't as reliable in the long haul as most boards in the $75-200 range (there are exceptions to that rule-of-thumb going both ways so don't just pick on price). Premium (over ~$200) motherboards are often going to offer so many gadgets and features that they will overwhelm the user with complicated BIOS, switches, settings, etc. These sophisticated motherboards often fall into the "Cadillac" class of problems. More features can wind up being more things to fail or more things that can potentially be set up incorrectly.

Always do your own legwork to ensure things will fit!

GPU length compatibility will be listed on the manufacture product page for any reputable case.
GPU length will be listed on the GPU product specification page.
CPU Heatsink height compatibility will be listed on the manufacture product page for any reputable case.
Clearance for RAM and other components under the CPU heatink, and the total size of the heatsink should be listed (diagram) on the manufacture product page for the HSF. Observe the position of the CPU socket on the motherboard and tall components on the motherboard to ensure that the planned orientation of the heatsink to be installed will not interfere with the case, case fans, tall components etc.
Height of the RAM modules selected should be available on the data sheet for them. (this is a common area of interference with aftermarket CPU cooling).
Another (less common) interference is the CPU heatsink with drive mounting. This can occur on more cramped microATX cases when used with motherboards that have their CPU socket placed very far "forward" on the board. OEM heatsinks typically don't interfere with any cases/RAM/drive-mounts, but they aren't as effective and tend to be noisier than nicer aftermarket options.

FYI: There are many microATX cases that can fit VERY long GPUs (longer than anything made), as they have their drive cages oriented above and below the expansion slot region of the case.

MiniITX and low profile mATX builds introduce much tighter restrictions for the fitment of PSU (which sometimes has to be an oddball size), HSF, GPU, drives, etc.
Full towers introduce issues with cable lengths (often coming up short on the length of the power connections for the motherboard, depending on the placement relative to the PSU in the case).

------------

Check out the Fractal Design Core 3500 if you are interested in a large ATX Mid Tower that is really easy to build in. With nearly a full inch behind the motherboard tray, even a monkey could establish clean cable management. The case is slightly wider/taller/longer than traditional mid-towers, giving it ample space to work in. The conservative drive cages, leave a very good wide open unobstructed path for airflow, and room for long GPUs.

For a traditional but modern microATX build, check out the CM N200. It will require some consideration of CPU HSF limits, but supports long GPUs comfortably and offers good cable management and airflow option in a compact case.

For a non-traditional compact build with good GPU size support that is relatively easy to build in, check out the SilverStone Sugo SG10.