So you're invisible and carrying a helpless creature? Here's what could happen…
Dungeons and Dragons 3.5 doesn't allow a creature to interpose itself between an attacker and the creature's burden, much in the same way that a creature can't carry, for example, a barrel or a coffin and claim the object's providing cover. Further, the system isn't granular enough to handle turning one's back on one's foe to take a hit for someone or something else, and, anyway, getting cover (or granting it) to something is largely unique to a special use of the tower shield, not just anything (or anyone) that's being carried that also happens to be bulky. Nonetheless, as can be seen below, it's actually kind of lucky that the game doesn't seem to consider a helpless creature much of a creature. (When engaged in combat, friends and foes alike grant each other soft cover all the time, but carrying a helpless creature follows different rules.)
The Rules Compendium on Sharing Spaces says
You can freely enter a square that contains a helpless creature, unless the DM rules otherwise, sharing that creature’s space. If you’re in a space with a helpless Small or larger creature that ceases being helpless, and for whatever reason that creature can’t share spaces with you, the creature must be or remain prone, attempt to grapple you, or leave your space at its first opportunity. It provokes attacks of opportunity as normal for what it does. (62)
And it says, "You can… share spaces with a creature you’re… carrying… (95). Finally, on Carried Creatures says
A Small or larger creature can carry a Tiny or smaller creature, which then shares the carrier’s space. If the carried creature is visible to an attacker, it can be attacked as if it were a carried object, including the benefit of the Improved Sunder feat. The carried creature uses the higher of its carrier’s or its own Dexterity modifier to determine its AC. (142)
An unconscious creature has an effective Dexterity of 0, by the way.
The size limits above technically prohibit carrying creatures bigger than size Tiny, but in this reader's opinion this is an oversight geared toward, for example, allowing the typical familiar to be worn as hat and not supposed to disallow, for example, a fireman's carry. Hence a reasonable house rule allows creatures to carry helpless creatures of their own size category or littler. (Tables I've played at have allowed picking up helpless creatures of the same size category without feeling the need to formally house rule the Rules Compendium.)
As no mention's made of them being lost, you retain the benefits of being invisible despite carrying the other creature, but, no matter how quiet you are, this DM would have reasonably intelligent foes assume that you occupy at least one square (you know, the one with the floating unconscious dude in it) and launch attacks accordingly, unless perhaps the party had previously demonstrated comic book-style telekinesis or casual use of multiple unseen servants. Also, carrying capacity might limit the weight of a creature you can carry while retaining your Dexterity bonus to Armor Class.
Another DM may require the helpless creature be instead grappled then moved. Fortunately, this is usually easy. Unfortunately, this would likely qualify as attacking the helpless creature, ending an invisibility spell.
In Dungeons and Dragons, Third Edition an attack against a foe with cover could hit the cover (PH (2000) 213); the Dungeons and Dragons 3.5 revision eliminates this rule.
…But you might be on your own
The game makes it really, really complicated for a creature to carry another creature. What mightbe preferable is first either taking a move action to pick up an item (i.e., in this case, the helpless creature) or taking a move action that provokes attacks of opportunity to move a heavy object (i.e., again, in this case, the helpless creature—no offense) then taking a move action that provokes an attack of opportunity to store the creature in a bag of holding or whatever, like sheathing a weapon. If rescuing fallen foes while invisible all the time, I urge you to spare the DM and yourself some grief and get the bag of holding forthwith. Just be sure to free the poor creatures stuffed in the bag before they suffocate.