Simply, it is not simple.
As you have done you can fly into the country and fill out the little white piece of paper with your info. They took half when you came in and you need to keep up with the other half until you leave. Fines are levied more often than not if you overstay 90 days but they were still working on getting a nationwide computer system to check the total days within 180 number.
Now, the law is 90/180. OK, clear enough but what about all these guys staying in there longer who aren't married to Ukrainians, aren't working for multinationals and those guys who just drift around the country all the time?
The law is not enforced consistently. There have been a few people turned back at the border for violating this rule but the majority get in and out with only small hassles.
Further, in order to stay over 90 days, even with a visa, you're supposed to register at the OVIR. Great, except that they will want to see either an invitation or a signed lease from your landlord and properly registered with the Zhek (Housing Administration office). These can be difficult to get from your landlords as itdocuments the property as being rented.
I received my 5 year business visa in Krakow and yes, as of a year and a half ago you got it back before 12 if you got it in there by 10 and then went to the bank to pay your fees. Cost was $165.
You cannot get residency until you have been married to a Ukrainian citizen for two years. Yes, it's screwy but they kept letting the married guys register at the OVIR under various visas until the two year period was up.
Even with the 5 year visa you still must register at the OVIR, pay your insurance and jump through all the hoops.
This still doesn't allow you to work or stay indefinitely however.
The bottom line is that there are laws which are vague and not enforced consistently.
Hope that helps.