It must be done in the editor (the middle option, when opening the game). After opening the editor, you have to click on ,,Modifications" option and choose the mod on which you have problem. I would recommend watching some tutorials on youtube, before opening editor - there is a lot of stuff you woudn't understand. I'm just gonna in this comment guide you on how to fix these things. Anyways, you'll need to open the map you want to edit (Rebember, that reuploading the mod you edited is highly prohibited). In top left corner there should be few options. Move cursor on ,,Map" -> ,,Load Map (has to be clicked) -> click ,,No" on the pop up screen (it's for saving a map. The one you start on, when opening editor is the default.e4m place, on which there is nothing, so no need to save it) -> Choose the map you want to change. Keep in mind, that the missions in the editor are not placed like when you open the game. Do these things:
- Railway Bridges - I had to raise them up. To raise or lower objects you have to hold left mouse and ,,alt" key,
- Platforms on train stations rotated in an awful way - I just simply rotated them. Same applies for railings, which are also rotated like platforms,
- Road Bridges - You can't fix it in the editor. I decided to replace models and prototypes of bridges with the one from Base Game by copying files. It worked (the texture did not changed however), but i had to do one other thing: In last Mission (Terrorist Attack: Dirty Bomb) the bridge through which units enter and leave the map doesn't have a ,,Em3" in their name in the editor (bridges with it come with this mod). Before or after changing bridges by replacing files i had to replace bridge on that map with the one that had Em3 in it's name. Why? Well, before replacing files with bridges the ones with with Em3 tag look exactly the same as the one without,
- Railway crossing barriers not working - Their default animation has to be set to ,,opend", otherwise they'll always be closed. Click on railway crossing barrier, then ,,Properties" and then in bottom left corner of the window, that should pop up there are all avaible animations for that object/vehicle/person etc. Choose ,,opend" and then ok.
Don't forget about saving the map.