What you're referring to is called a composite. Trust me, you can't afford it.
Here's why:
The lab is going to conform your edit based either on your EDL (edit decision list) or your work print which you will submit back to the lab. If you have fades, dissolves or any other optical cues, the lab will make A/B rolls. They will match the encoding on the film negative to your 'cut', meaning they will physically cut your negative and assemble it as listed in your EDL or based on your work print cut.
The whole process goes like this: Negative Original -> 1 light work print
(You edit using your work print)
Then: Negative Original -> Answer Print (color timing corrections are made) -> Final Print (release print).
This is called posting photochemically, and from your description, this is what the lab is doing to your film. Now, if you want special effects added into the final print, the lab must be equipped to composite your CGI's onto the answer print and be able to change your color values within your electronic file to match the timer's light settings. In the old days, this was done using a process called optical printing. It was extremely technical and difficult to pull of convincingly as it required either locked-off shots with certain areas within the frame matted so they remained unexposed which were then re-exposed later with the effects footage; or motion control systems were utilized (Star Wars pioneered those systems, and they optically printed their effects).
Today, productions use either blue or green screen backgrounds so that they can manipulate action on many different layers and then composite the final images through a high resolution file, which they then re-expose back onto a negative strip of film. Doing this properly requires scanning each frame of your negative at a very high resolution (4K is quickly becoming the standard). This is very time consuming and very expensive.
To bypass all of this, ask your lab if you can supervise the answer print and then have the final print provided to you in high res video. You can then composite the images yourself and do your release on DVD.
If you plan to release your project on film to be screened through a projector, you cannot afford the process, as the cost would be in the thousands. More so if you have a lot of film (not a short).
