The Apple iPad supports the following video codecs:
H.264 video up to 720p @ 30 frames per second
- Main Profile level 3.1 with AAC-LC audio up to 160 Kbps, 48kHz, stereo audio in .m4v, .mp4, and .mov file formats
MPEG-4 video, up to 2.5 Mbps, 640 by 480 pixels @ 30 frames per second
- Simple Profile with AAC-LC audio up to 160 Kbps, 48kHz, stereo audio in .m4v, .mp4, and .mov fileformats
Motion JPEG (M-JPEG) up to 35 Mbps, 1280 by 720 pixels @ 30 frames per second
- Audio in ulaw, PCM stereo audio in .avi file format
If you can give us some more details about the format you created your custom videos in, we can try to guide to converters to get it into one of the acceptable formats
As to putting them onto the iPad -
Detailed instructions in this article
can a video be transferred to iPads?