The simplest way to accomplish what you want may be to drag the file from the bin to the timeline. Then split at the IN and the OUT points of the commercials. Click in those split-out areas and press the DEL key on the keyboard. Export the result as a Video file in the mp4 format.
In order to see the timeline clips individually you may have to expand the timeline, using the slider at the bottom-right of the window...
. To position the clips use the horizontal scrollbar at the bottom... 
Some insights...
Once a clip is imported into the media bin (top-left) it stays there. After being placed on the sequence, whether via method 1 or 2 above, it can be further trimmed if need be. Effects, transitions, etc. can be added. Don't delete the clip in the bin. In most cases it's not affected by changes made to it on the timeline.
Save Project or Save Project AS creates a VPJ file that instructs the program what to do. Do not move or delete any source files. For your protection, Save Project File AS routinely, giving it a unique # or name, so as not to overwrite prior saves. Using Save Project Files (no AS) will overwrite. From the HOME tab, that choice is available by clicking the caret to the right of the Save Project button on the toolbar.
It's this file that can restore the project at a later date - your project protection. A VPJ file cannot be played.
Exporting is an entirely different operation. It creates a playable file from the clips on the sequence. Export choices are available from the toolbar and via the top-left Menu.
If you want an mp4 format file choose Video File. This window appears...
The defaults are often fine, but can be changed to any number of formats, resolutions and frame rates. Auto Match is a best guess, based upon content.
