Screenplays are much different than other narrative forms in that they are composed of short scenes compiled into a string to form the final whole. These scenes are somewhat self contained, containing headings and descriptions for what happens and finishing with proper closings that signal clearly that the specific scene has come to a close. The common format for screenplay is in place here so that people are able to identify these directions as well as to quickly acknowledge where the beginnings and ends are. When separating your scenes in your screenplay the format has a standardization that the industry recognizes.
In The End
Once you have come to the close of a master scene you have to clearly state that it is finished. This is usually done with a combination of finalizing actions from the characters, a shift in perspective of the camera, and a transitionary notice. This can be something such as FADE OUT of CHARACTER EXITS. Secondary scenes are often a little different as are cut-aways because these are often just short descriptions.
When you are looking to separate master scenes you need to create a significant amount of space between the text blocks so they immediately appear separate. This usually requires a standard of three blank lines so that they are obviously completely different. Older scripts often use less than this, but now it is important to go three or more because often times professionals in the field will be reading through very quickly or just scanning the text. They need to have an impression of separation made.
It may seem that labeling or numbering the scenes will help with this, but that still should not be done on a spec script. The unit production manager will do this to the script during pre-production as this is not the job of the screenwriter. That type of organization is strictly to aid the production as decided by people specifically involved with the actual filming. You can make sure that the following scene has the correct master scene or secondary scene headings so that people will see that it takes place in either a different place or simply a different time frame.