Hi,
I’m wondering how to manage tilemap objects to keep my project clean. I’ve created tilemap with different layers: ground, tilemap objects (not usable) and layer with collisions (walls, bottom of the trees etc). Now i would like to put many scriptable objects and enemies. What should i create empty object and store every single prefab individually?
I suggest that you “manage your tilemap objects” and when they get messy, clean them up. 
This makes it sound like you haven’t actually started.
If you’re unfamiliar with the Unity asset / scene / prefab environment, fix that first. Here’s how: Work through half a dozen tutorials until you can stick your finger randomly on any part of the game and explain to your dog (see my avatar?) what it does and what it is for.
Until you have done that, everything typed in response to your question above will either be:
a) irrelevant to your undetermined and undefined actual future implementation
b) be inactionable by you because you haven’t familiarized yourself with the problem space.
EDIT: I see I have posted this to you before, but it still applies and it will always apply:
Tutorials and example code are great, but keep this in mind to maximize your success and minimize your frustration:
How to do tutorials properly, two (2) simple steps to success:
Step 1. Follow the tutorial and do every single step of the tutorial 100% precisely the way it is shown. Even the slightest deviation (even a single character!) generally ends in disaster. That’s how software engineering works. Every step must be taken, every single letter must be spelled, capitalized, punctuated and spaced (or not spaced) properly, literally NOTHING can be omitted or skipped.
Fortunately this is the easiest part to get right: Be a robot. Don’t make any mistakes.
BE PERFECT IN EVERYTHING YOU DO HERE!!
If you get any errors, learn how to read the error code and fix your error. Google is your friend here. Do NOT continue until you fix your error. Your error will probably be somewhere near the parenthesis numbers (line and character position) in the file. It is almost CERTAINLY your typo causing the error, so look again and fix it.
Step 2. Go back and work through every part of the tutorial again, and this time explain it to your doggie. See how I am doing that in my avatar picture? If you have no dog, explain it to your house plant. If you are unable to explain any part of it, STOP. DO NOT PROCEED. Now go learn how that part works. Read the documentation on the functions involved. Go back to the tutorial and try to figure out WHY they did that. This is the part that takes a LOT of time when you are new. It might take days or weeks to work through a single 5-minute tutorial. Stick with it. You will learn.
Step 2 is the part everybody seems to miss. Without Step 2 you are simply a code-typing monkey and outside of the specific tutorial you did, you will be completely lost. If you want to learn, you MUST do Step 2.
Of course, all this presupposes no errors in the tutorial. For certain tutorial makers (like Unity, Brackeys, Imphenzia, Sebastian Lague) this is usually the case. For some other less-well-known content creators, this is less true. Read the comments on the video: did anyone have issues like you did? If there’s an error, you will NEVER be the first guy to find it.
Beyond that, Step 3, 4, 5 and 6 become easy because you already understand!
Finally, when you have errors, don’t post here… just go fix your errors! Here’s how:
Remember: NOBODY here memorizes error codes. That’s not a thing. The error code is absolutely the least useful part of the error. It serves no purpose at all. Forget the error code. Put it out of your mind.
The complete error message contains everything you need to know to fix the error yourself.
The important parts of the error message are:
- the description of the error itself (google this; you are NEVER the first one!)
- the file it occurred in (critical!)
- the line number and character position (the two numbers in parentheses)
- also possibly useful is the stack trace (all the lines of text in the lower console window)
Always start with the FIRST error in the console window, as sometimes that error causes or compounds some or all of the subsequent errors. Often the error will be immediately prior to the indicated line, so make sure to check there as well.
Look in the documentation. Every API you attempt to use is probably documented somewhere. Are you using it correctly? Are you spelling it correctly?
All of that information is in the actual error message and you must pay attention to it. Learn how to identify it instantly so you don’t have to stop your progress and fiddle around with the forum.