Yes, any changes you make using the forms interface are saved. There is sometimes a difference in where they are saved if a worksheet is bypassed, but if you are editing an imported form like a 1099 or w2, this won't ever happen.
Do be sure you are filling out the form just as it will be received by the IRS, who get it directly from the sender.
Do go over your forms, as you have, to be sure they are as they should be.
Do NOT enter corrections to the data your "sender" might have made on the form. Anything like this must be dealt with differently so that the IRS doesn't flag your return as containing an error. Their computers are very good at cross-checking forms like w2's and 1099s!
