Gracies Story

I thought Gracie was a kitten about 8 months old.  The vet said she is 2 or 3 years old.  I have no idea now long she has been feral but she traveled with a long haired black cat which is so feral I cannot get close to it.  Gracie would immediately let me pick her up.  She is orange calico.  I have a Siamese male eight years old and they would be so nice together.  My challenge now is to be able to trust Gracie to always find and use her litter box (she made a mess on carpet but was cleaned up immediately) and hopefully let the two of them Rudy and Gracie interact together.  At this point, there is some hissing and low growling.  Any suggestions would be greatly appreciated.

Cats learn how to use their litter box almost instinctively but if you are concerned that Gracie needs some encouragement in that direction, you might try using Dr. Elsey's Precious Cat Attract Litter.   
You might also need to add at least one more litter box - the usual rule of thumb is one box per cat, plus one.  Here is an article on litter box issues that might help you. 
[article="32366"]How To Solve Litterbox Problems In Cats The Ultimate Guide  [/article]
In terms of getting along with your Siamese,  did you go through an introduction process at all?  It's usually recommended that you put the new cat in her own room for awhile and go through a gradual process involving scent swapping and gradually increasing contact.  Below is an article on cat introductions that should help.. 
[article="32680"]How To Successfully Introduce Cats The Ultimate Guide  [/article]
Unless they are basically getting along except for a little hissing and growling, you should probably separate them and start the introduction process from the beginning.  Since you're not describing any actual fighting, there is a very good chance they will get along just fine in the end.

EDIT:  I think it's wonderful you've rescued this little girl.  We would all love to see photos of both her and your boy.  What's his name?

This is a little more on Gracies Story.  She is in my upstairs bathroom now and will venture out now and then.  I have a "Kittyshack" in there for her and she loves it.  She practically lives in it.  Rudy, the male Siamese, has let her know that this is his house and his rules.  She will come out of the bathroom (which I would like to reclaim) but when he comes around, she runs back in there.  They have gotten about a foot apart from each other but then she will holler at him and he goes away with expression like "Oh, well."  He is rather put out with me because he said: " You big cats (cats think we humans are just big cats) you bring me in here, get me fixed, and then you bring me a blonde."  It is interesting to watch the two of them in that Gracie (as far as I know) has always lived feral and Rudy since 6 weeks old has been in house.  When I give them treats (together - out of each hand) he very gently waits for her to finish hers before he will eat out of the hand that is his.  She on the other hand butts her head against my hand to get the treat dropped and then she will gobble them up quickly. 

Thank you for the update!  It seems things are moving in the right direction.  Rudy sounds like a true gentleman at treat time!