Instead of first using the ugx script placer to create a new project, I use the radiant in the launcher and clicked "new file". I then proceeded in making my map without realizing that for it to work I need to use the script placer first. If there is any way to essentially copy the .map file that radiant has created and put it into a folder created from the script placer, that would be very helpful as I have worked really hard on this map and am kind of new at this but I would like to avoid restarting at all costs.

Copy .mapfile to a safe spot, like desktop, run Script Placer and have it overwrite everything, then drag the .mapfile back in map_source and compile that

Hitman's directions are going to give you a few problems if you haven't taken care of these when starting your new map:
a) Player spawns (which are exactly as they sound)
b) Worldspawn settings (what the suncolor looks like, the sun placement for shadows, etc)

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Here are my directions assuming you are using the UGX script placer:
1) copy the .map file somewhere safe and copy it to your map_source>prefabs folder
2) create a map using the UGX script placer with a 'set up' map
3) open the 'set up' map that was just generated and delete the box walls surrounding the player spawns
4) right click the 2d window in Radiant and insert the prefab of your map (be sure to align it so that spawn is where you'd like)
5) with the prefab highlighted you can 'stamp' it in to your new map, making it editable. The stamp looks like it does below

Spoiler: click to open...

[close]

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The key advantage to this method is that it preserves the player spawns and world spawn settings of a 'set up' map

Maybe he has all of those, his question was only about "how do I keep my progress, if I create mod now"

I actually think i figured it out. In UGX script placer the is an option called "Map Source". If you select custom you can choose the location of the .map file it uses when creating the map folder.