Sure you can leave them on. Whatever you like - I find them a bit chewy.

This samequestion has just been mentioned here in several threads. If you don't mind having small red 'twigs' in your sauces, then its fine to leave them in. Once the tomatoes are cooked, the skins fall off, and roll up into little red sticks. These, for some people are not a good texture in the mouth. I tried to puree them with no luck even after running in a Vitamix blender for several minutes. Now, bcause I use a Vilaware (now called Roma) the machine will remove all skins, and as a bonus, all the seeds from the tomatoes even before they are cooked.

The peels are removed because that is where most of the bacteria is. You can leave it on, but it will be like little twigs, like Ken says. I don't like them in my food.
Be sure you add the required bottled lemon juice or citric acid for safety in both boiling water bath and pressure canning.
The link below will give you the instructions for all kinds of tomato products. I don't know if you are raw packing, hot packing, etc. If you are raw packing, not adding water, in a BWB you process for 85 min. Some folks make the mistake of trying to use the ones with water added and not processing long enough. I don't know of anyone who adds water to their tomatoes. Crushed tomatoes have a shorter processing time if you want to go that way.
They are packed hot.
Less shrinkage in the jars, too, than a raw pack.

Here is a link that might be useful: Canning tomatoes.

Just a note that the Ball Blue Book was very helpful to me when I first canned tomatoes (and now). It has some nice drawings in it that help clarify procedures.

I am new to this canning of tomatoes. I followed the ball book recipe to a T. My question is= My jars have about 1 inch of clear liquid at the bottom. Is this normal? Are the tomatoes okay? Did I do something wrong?

No you didn't do anything wrong. There are certain enzymes and pectins in tomato products and getting the water not to settle out has to do with the temperatures you keep your tomatoes when handling them. I used to get water in the bottom of my jars occasionally even when making tomato juices, but found this information. I'll link to it.

The product is still quite safe and it's not a biggie, but if you want the product to be more homogenous please have a look at the link. My tomato sauces this year are a thing of beauty and are not settling out at all.

Here is a link that might be useful: tomato canning information

Quite normal to see that clear liquid. Its common when your using tomatoes that contain a lot of water in them. I like using a meatier tomato type, and scoop out some of the liquid and seeds before they are either canned or are put through the Villware strainer. Skins I hate, as they even show up after 'digesting them', if you know what I mean. High fiber they are, but how useful to our digesting I have no clue.. They just don't look appealing when you see them in the bottom of the spagetti. Tip- give those jars a quick shake before selling...

Heres a quick way to enjoy them too. Slice some whole tomatoes and place on several layers of paper towels to soak up some liquid, while you sprikle salt on them. Make a batch of bread dough, spread out to the shape of a big pizza, spread it with olive oil and oregano and/or basil, then add the drained tomato slices close together, sprinkle with mozzarella or other favorite italian cheeses and bake. OUT OF THIS WORLD!!

Calliope,
I read your link but I'm still not super clear on how you exactly what you are doing with your tomatoes. Do you warm them whole for 5 minutes - no more, and no less - before processing?
Thanks, Melly
(still hoping to get some tomatoes)

Melly, that's what I'm wondering, too. It's got you heating the first tomatoes -while- chopping the rest, then heating the entire thing for five minutes. But doesn't that make the first ones in heat for too long?

I run the tomatoes through a food mill. The skins that are left I put in my nutrabullet with some of the juice, pulvarise them and put them back in the sauce

when I can my tomatoes for sauce or juice I like to put them in a blender after cutting off any blemishes and the core. Then I cook them in a large pan for 45 minutes, poor the sauce or juice in clean hot qt. jars and then water bath them for another 40 to 45 minutes. Take them out of the water when its done and let them rest for 24 hours on towels. Make sure the center of the lid pops and it down instead of up. You can use them over the winter.

I always peel and cut up and cook my tomatoes and will run them through a food mill before canning. I don't want to waste space canning up water. I have done it this way for years.

I have made sauce and left the skins on, but I have always run them through the food mill and that makes if better. I prefer without the skins.

For some reason, the tomatoes from the farm is year seemed to have a much tougher skin than in past years. Maybe a different variety. or weather? Also they seem to plagued with those hard green hearts in the middle. Have seen it happen in other years but more so this year. I don't waste room in my jars with those green hearts. They will never cook down. I get them out first