OK, Davy... you REALLY need a decent book or video on training Border Collies. First, keep her AWAY from chickens, until she's a lot older. At this age, I concentrate on "no chickens", "no cats", etc...
I recently bought a video on training BC's, and while I disagree with some of it (he's a pure sheepdog trainer, and he kennels his dogs unless they're working or being trained- I just can't do that!), it's an excellent video on starting them on livestock and herding commands. I know there are plenty of books on training BC's, but I don't know of a title offhand of a good one...
Second, the natural instinct for BC's is to bring the flock TO YOU! Driving- pushing them away from you, with you behind them (the more common way to handle most animals except sheep) isn't "natural" for them. It must be taught. English Shepherds tend to be a bit different- while they also may have a natural tendency to round the herd/flock up and bring them to you (we have to caution Dixie to "stay back" a lot yet), it isn't as hardwired into their brain as it is in the BC's. ES tend to "help" their human, and at least the ones I've had learned what we needed by watching us, and helping where it appeared to be most needed.
Sometimes they were wrong, especially as young dogs, but a bit of warning, or guiding them with a light, long line, worked.
Now, you really need a "potty word"! This means, you take her out on a leash, you don't encourage any side excursions or "fun" until she GOES... and when she does, you use the "potty word" and also praise her. It can be anything that works for you- a silly phrase, whatever- just don't make it a common phrase you might use at other times- don't use "Hurry up", for example, unless you never use that at any other time! LOL!
What do you do when she messes in the house? While "punishing" a pup who "can't wait" is futile, they DO have to know it's not acceptable. I still can't imagine trying to house train a pup without papers or another "allowed" indoor potty area... not for the first 4 months or so. The problem is, the more she uses the floor, the more ingrained the habit gets. Seriously, it's time to crate her in the house (or set up an x-pen or gates in one SMALL area), and then IMMEDIATELY put her outside when you let her out of the crate. Leash her, use the "potty word" and then praise her lavishly when she "goes".
We've got one male pup left, and we're planning on keeping him and starting his herding training- in about 8 months. Until then, we mostly are working on basic commands (still pretty impossible, as he's way too wiggly yet to do much. He does walk on a leash, he knows "sit" (but only does it after he's worked all his wiggles out!), and comes fairly reliably. That's about all I expect at this age. I'm taking him for truck rides, teaching him to stay out from underfoot (hubby's cane both makes that a necessity and also has made it very easy- he just pushed him away with the cane when he got within tripping range, and he now stays about 2 feet from us when he follows us around the farm.
Aside from "no chickens" and "No cats", we're teaching "no horses" (tails are really tempting for pups, and while my mares are pretty pup savvy and patient, all it takes is one kick to ruin a good pup) We also are teaching "wait" and "stay" (as I've mentioned before, "wait" means "stay where you are temporarily". I encourage them to "wait" until I use the "that'll do" command... but I don't punish them at all for breaking early. I use this mostly in doorways, at stairs (I don't want a dog pushing past us on the stairs, either way... it's a good way to take a bad fall), and when I'm driving machinery and don't want them following.
When coming in the house, even if I'm going to let the pup come in (we bring him in for 2-4 hours a day, usually... we've had precisely one puddle in the house!), I tell him "wait"... I enter the doorway, get out of the way, then say "ok, come". And he comes in. This is so routine at this point, that he automatically sits outside the door until he's "invited" in. (some of this is "puppy submission"- I fully expect at some point for him to start saying 'hey, I'm coming in anyway- it's crappy out here, and that house is warm"!) The older dogs pull that on occasion (you ought to see the kitchen floor when all three of them do it in the rain!) IOW, just because they KNOW what a command means, doesn't mean they will absolutely do it every time! They're individuals, and they're SMART. Only you can decide how much you need solid obedience, and how much "mischievous selective deafness" you can tolerate.
Rather than working on rigorous obedience stuff at this age. PLAY with her. Balls, tug-of war (not a lot of that, especially if she's showing any signs of dominant behavior), race her, scoot around and let her herd you (use the "that'll do" command when you're done with that, and enforce it!) Our dogs love floppy stuffed animals- although they "kill" them on a regular basis and I have to make or buy more!
And if she's testing you by running away, or otherwise making it difficult for you to enforce commands, start leaving a long (about 25'), light (clothesline weight or even a bit lighter) line on her collar when she's outside, especially if you're working with the chickens or other "tempting" things. If she ignores you and keeps doing something she shouldn't, you can step on the line and pull her in to you, repeating "that'll do" or "here".
ONE instance of them "getting away" with ignoring a command will mean a hundred repetitions with enforcement before they forget they "got away" with it!
You can do this! She's a smart pup, and right now, it sounds like she's outsmarting you a bit. Remember she's still a baby, and give her a chance to mature a bit before demanding too much in the way of training. But you've got to get control of the housebreaking now... and that means a crate or pen, papers and a "potty word".
If you've got any specific questions, you know where to find me!
Summerthyme