We want to file as married filling separately, how to handle the 8949

I would allocate them 50 - 50 by reporting category totals instead of individual transaction.  Each of you  can report 50% of each category total on your tax return.  You will need to mail a copy of your Form 1099-B and Form 8453 to the IRS.  Include a statement explaining that you are filing MFS and each of you is reporting 50% of the transactions.  To report category totals:

 

To do so,

• Click on Search
• In the Search Window type 1099-B 
• Click on "Jump to 1099-B" 
• Click + Add an Account (if the account you were trying to download is showing, delete it first)
• Answer Yes to "Did or will you receive a 1099-B form or brokerage statement for these sales? " 
• Click on "I'll type it in myself"
• Select your Bank or brokerage and click Continue 
• On the page with "Tell us about your 1099-B sales for this Charles Schwab account" answer the question about employee stock & the number of sales, etc.
• click the button "Let's enter a summary" 
• Enter your Investment Sale information and repeat to you have entered for each category.

After entering all your category summaries,  Look for "To finish reporting these sales, follow the mailing instructions" and click on the link for these instructions: 

 

Take a moment to double-check that your statements are complete. For each sale listed, there should be:

•  - A Description
•  - Date Acquired
•  - Date Sold
•  - Sales Price
•  - Cost Basis
•  - Gain or loss for each sale
•  - A based on how the sale was reported to you and the IRS

 In some uncommon cases, there will be an adjustment code and adjustment amount.

 NOTE: Any sales summaries that include only Box A or Box D sales, and which have no adjustments to gain/loss, do not need to be included on a statement mailed to the IRS.

 Here's how to mail your statements:

 If you are e-filing your tax return, then mail your statements along with Form 8453 to:

Internal Revenue Service

Attn: Shipping and Receiving, 0254

Receipt and Control Branch

Austin, TX 73344-0254

If you are not e-filing, then mail your statements with your entire tax return to your local IRS office.