And even if your new allies decide to attack your enemy on their own, they will be in a "separate" war. It will be listed separately on the alliances screen, and you will have separate war scores for the purposes of determining who is "winning" each war. You would, however, be able to both lay siege to an enemy province at the same time (though only one -- the one with highest ranked commander-- will gain control of the province if successful)
It's really a separate question, but in general, allies are usually more trouble than they are worth for most wars. They tend to bring way too many troops to a siege, and may "steal" the siege from you by having a higher ranked commander. Save the allies for the wars against overwhelming enemies where it's life or death, or for wars where they can open a "second front" that may keep the enemy busy and where they won't interfere in your own operations.
If you are in over your head in the current war, stop and evaluate the situation with a ruthless streak. First offer a peace just to see what your relative war scores are -- do you have any stars at all? (Obviously cancel the offer rather than sending it!) Second, rather than concentrate on what you'd hoped to get out of the war, evaluate what you can still salvage. Does he have any provinces that you can take very easily and quickly (e.g. an unfortified city or a minimal fort that you can siege heavily or assault) -- that might be enough to give you a star or two in war score. Can you buy your way out of the war with a relatively small amount of cash? Can you buy your way out of the war by giving up a province that does him little good (e.g. no connection to his own territories, maybe even one of your core provinces that will give you a permanent CB against him for the next round of wars) ALso, while you are doing all of that, assuming that he has superiority of army numbers or quality, avoid open combat -- let him siege your provinces and hopefully attrit while you do whatever you need to do.
One of the biggest mistakes one can make is to hang on in a long-running slugging match of a war that drains your resources for very little potential reward. In big world conquest games, I used to "roleplay" a certain amount of vindictiveness against the little one-province nuisance countries who would DOW me. If I didn't plan to annex them yet, I'd still often take their capital just to avoid paying them the 250d they asked for peace. Then I started to calculate how much it was costing me in attritted armies and extra military maintenace (during wartime your maintenance costs are increased).
