You don't need any special programm to swap skins. It's just a simple case of copy/paste and renaming files.
For this specific one, you have to backup the Spider-man skin you want to replace. Those can be found in the actors folder in the main directory under the following names:
Scarlet Spider: 0903.igb
Stark Armor: 0904.igb
Now rename the spiderman2099.igb file to the one you're replacing. Let's say you're taking out Stark Armor, then you should change spiderman2099.igb to 0904.igb . Paste the new 0904.igb in the actors folder, replacing the old one.
For the hud, it's a similar procedure, but obviously replacing the hud file in the respective hud folder.
For more info, check this topic: http://marvelmods.com/forum/index.php?topic=698.0