You can print the e-file instruction letter in the e-filing steps. When you come to the screen E-filing - Topics, use the option Print Return and E-file Documents. On the E-filing - Print screen, use the Click here link at the beginning of the first paragraph for instructions addressed to your client. The Print Selected Items button will give instructions intended for the preparer.
To choose whether the instruction letter to your client is about mailing the paper return or e-filing:
You can then print the instruction letter directly with the printer icon above the form in the blue bar, or from any of the commands to print the return (the Print button on the toolbar, from Preparer > Print Returns, from File > Custom Print or Print Client Return), or during the filing steps. When you get a Print Center window, make sure you are on the Client Return tab and that you specify at least one copy for Federal Instruction Letter. Then click the Print button at the bottom.
For the state return, the instructions are the same as above, but at step 2, you will choose Preparer > Instruction Letter > Edit Client Copy > State > and then choose the state. Step 3 will have slightly different language for the options under a section labeled in most cases "Indicate how this state return will be filed."