Can I deduct employer retirement IRA contributions after I already entered it in from my W-2 or is that deducting twice?

What code did you have in Box 12 of your W-2? The ones below are types of deferred compensation that are normally indicated on your W-2. 

• Code D -- Elective deferral under a 401(k) cash or arrangement plan. This includes a SIMPLE 401(k) arrangement.
• E -- Elective deferrals under a Section 403(b) salary reduction agreement
• F -- Elective deferrals under a Section 408(k)(6) salary reduction SEP
• G -- Elective deferrals and employer contributions (including nonelective deferrals) to a Section 457(b) deferred compensation plan
• H -- Elective deferrals to a Section 501(c)(18)(D) tax-exempt organization plan

or 

• Code AA -- Designated Roth contribution under a 401(k) plan
• BB -- Designated Roth contributions under a 403(b) plan

None of these are deductible anywhere on the return as they are already getting a tax deferred benefit.