I did that black project mission and I want again to go inside that area but there is no way to go there. So how do I go inside of Area 69 if I want to?
According to gta.wikia.com it is possible to re-enter the underground through glitches:
The easiest way to enter the base is to use a Blue Hell glitch with a Jetpack equipped. Once in the Blue Hell, fly towards the base. Once below, fall in the Blue Hell. Once deep enough, the player will be teleported at the bottom of the launch bay.
Another way requires a Freeway bike (easily found in Fort Carson). Once obtained, drive in Area 69 and find the vent (which CJ can use to breach in the base in "Black Project"). Stick the bike on the northern side of the vent, and have the bike face towards the south-west (since Carl will leave the bike on the left side, he'll step on the vent). Once done, exit the bike. Carl will step on the vent, and will suddenly teleport below ground, on a Minigun spot in the underground.
If the Freeway bug was chosen, go back at the entrance of the underground. Destroy the vent grate, then go at the entrance of the vent and press the button to enter a vehicle. If the Freeway is at the same position, Carl will go through the vent and hop back onto the bike, above ground.
Still using a jetpack, go to the large room where the first scientists are found (near the SAM control site). Enter the room from the underground entrance, then go on the first staircase on the left. Once here, go upwards with the jetpack. The roof is not solid, allowing the player to go through. Fly far away enough from the base, then fall into the Blue Hell. The player will teleport at ground level.
Here is a good video example: