There are some very fun ways to do two player drafting from a cube. I would not build a special, small cube for two player drafting, but just build a regular cube. If you end up drafting with two players most of the time, that's fine, but you have the option of more people playing.
Some of the ways that I've done two player drafting are:
1. Start with 10 packs of 15 cards, deal out three piles of five cards. Each player takes one pile and the last pile is flipped face up. Take turns swapping one card in your hand for one of the face up cards. Once both players pass, keep what you have in hand, remove the five face up cards and move on to the next pack. Alternate who gets to pick first.
2. Select 105 to 150 cards from the cube and put then in face down pile. Deal out three cards face down. The first player looks at the first card and may take that card. If he does then his turn is over and a new card is dealt out to replace the pile. If he doesn't take the first card then add a card face down to that pile and move on to the next pile. Again, the player may take that card or move on to the next pile. The same choice is offered for the last pile. If the last pile isn't taken, then take the top card of the large stack of cards. Each time the pile is replaced by a single face down card or a face down card is added to the untaken pile. Alternate turns and keep going until the original stack of cards in gone.
3. Start with 150 cards from the cube in a face down pile. Deal out a three by three grid of face up cards. The first player to choose may take all three cards in any given row or column. The second person may then take any remaining row or column. Set aside the remaining cards. Alternate who chooses first.
If you're interested in building a cube I would suggest checking out the Cube forum at mtgsalvation.com:
http://forums.mtgsalvation.com/forumdisplay.php?f=349
It is really valuable and a number of people that write cube articles for different MTG sites hang out there, along with a lot of other knowledgeable people.