Maintaining deviations from a citation style

I have numerous instances where I need to change the in text citation style from the default for a particular journal such as: (Smith et al., 2008) to Smith et al. (2008). Is there a way when inserting a citation, to specify the different style format, or does this change simply need to be had edited at the end of the writing process? 

The frustrating part here is that if I do the hand edits, then change to another journal citation style, all my had edits are removed and the format goes back to the (Smith et al., 2008) format. 

I feel like I must be missing something here. 

Thanks in advance

The EndNote output style’s  Citations template controls the display format of in-text citations. Automating the display would be alot easier than manually adjusting each one - plus unless the adjustment is done to the template itself, as you’ve noted, none of the hand-modified changes will “stick”.

To access the Citations template, go to the EndNote toolbar, select EDIT, OUTPUT STYLES, EDIT [name of the style you’re using].  In the output style’s dialog box, in the left column locate “Citations” then click on “Templates”. In the template window, move the left parenthesis to the right so it appears after the Author field. (If there’s a comma after the Author field, delete the comma.)  The idea is to encase the Year and Pages fields with the parentheses to get the (2008) effect in the citation.

Close the output style dialog box which will save the changes to a new file having the word “Copy” added to the file name. Adjust both EndNote and MS Word to use the new file.

Are you using EndnoteX5 and is this something you only want some of the time?  If so, then X5 has the option to convert the (Author, Year) to Author (Year) in the edit citation dialog (right click in the citation, edit citation, second option.