In the same way the photos were transferred to your iPhone, via the iTunes sync/transfer process.
iTunes does not store photos. iTunes serves as the transfer conduit only for transferring selected photos on your computer to your iPhone.
If you manually manage photo storage on your computer, create folder on your computer. Place the named folders of photos in this parent folder that you want transferred to your iPhone. Select this parent folder under the Photos tab for your iPhone sync preferences with iTunes followed by a sync.
To add additonal photos to your iPhone, place the photos in a new folder and place the new folder of photos in the parent folder followed by a sync.
Or place the additional photos in one of the existing named folders of photos in the parent folder followed by a sync.
To remove an entire folder of photos from your iPhone, move the folder of photos out of the parent folder on your computer followed by a sync.
To remove individual photos, move the photos out of the folder of photos in the parent folder followed by a sync.