I am confused by your question, you may also be confused.
You can make IRA contributions up to $7000 (if you are over age 50). You must also have compensation from working.
A rollover is not considered a contribution and is not part of your $7000 annual limit. If you did a direct rollover (direct from plan A to plan B) then enter the 1099-R and when asked what you did with it, select that you rolled it over to another qualified account. It's perfectly OK to have a $3144 rollover from plan A to plan B and also $7000 of new contributions to plan B, because rollovers are not counted in your contribution limit.
If you received a check from plan A, that is considered an indirect rollover. You had 60 days to contribute it to plan B, but you must tell plan B that it is a rollover when you send them the money. They may have a special form for you to fill out. If you received a check for $3144 from plan A, and deposited $7000 into plan B, you can treat it as a $3144 rollover and $3856 of new contributions, as long as you completed the rollover within 60 days.
If you did not tell plan B it was a rollover, or if you waited more than 60 days, then you don't have a rollover. You have a taxable withdrawal from plan A, and $7000 of new contributions to plan B. You will also owe a 10% penalty for early withdrawal from plan A unless you are over age 59-1/2.
