Fox, its time you paid a visit to the reference section and download Leon Marricks "Advanced Guide to Scenario Design" -this document will tell you all you need to know, and don't be put off by the title. Its a good read, and filled with all the information that you ask for, and a little more.
Now, your questions.
Yes, you can put basically all the .gif and .txt files you need in your scenario directory (civ2/scenario/imperialism in your case). Simply right click, copy, and paste as copy from your civ2 folder to your scen-folder. Then you can do all the editing in the scen-folder.
There are some exceptions to this, like the .dll files which will have to be in the main folder (these are the files containing the nuke eksplosion and leader pictures etc.), and a few other files, that are not normally altered. In far most cases, you'll do with copies of rules.txt, labels.txt, cities.txt, units.gif, terrain1+2.gif, cities.gif, and the .scn files along with the introductory txt. If you want to alter the sound, simply make a sound folder in your "imperialism" folder following the same procedure as above.
NOTE : you do not need to put unaltered files in your scen directory. If Civ2 cannot find the files here, it will simply use those in the root directory.
In order to make the .txt file work, make sure it is written in the right format. Then load in your savegame and save as scenario, with the same name. Quit civ, and start it again, then load your scenario. If it still doesn't work, there must be something wrong with the formatting of your text.
When you're finished with the scenario, it is custom to write a readme with information about the scenario, who made it, how to play it, how to install, who to contact. You can include credits for "borrowed" artwork or other things in this file.
Cities that are built by accident... It is a little awkward, but simple enough. And there is no easier way :
Reduce the city to size 1 (and NOT size zero). Press ctrl+c with the cursor on the city spot and a menu pops up. Select change size, and write 1 in the spot. Now press ctrl+d still with the cursor on the city spot, to kill all units in the city, if any. Then create an enemy units outside the city gates, using shift+f1 and the "foreign" button. Select human player from the cheat menu, and choose that tribe you just created a unit for. Select the unit. Conquer the city, which will be reduced to rubble in the process. Destroy (Ctrl+d) the unit you just moved. The city is gone.
In order for this trick to work, remember to select "Always wait at end of turn" from the game options menu when you design your scenario. Otherwise you WILL have units running amok, and it'll be impossible to concentrate on anything. When you need to change players, use the cheat menu "select human player" and you won't have any trouble.
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. Can I put a labels.txt in my scen. JUST for my scenario?
