I'm in the same setting. I mix and match, maintaining CO Gold mostly on trips to IAH, and through CLE to the midwest. However, for transcons, it's not worth connecting through EWR when AA, UA, and B6 offer nonstops. I just take whatever's cheapest for those. The higher status I could get by sticking to CO doesn't justify the pain of connecting at EWR. I therefore have 19K EQM on CO, 18K on UA, and 6K on AA so far this year. It could have been nearly 45K on CO, but it wasn't worth it.

Remember you do also have NW to DTW, MSP, AMS, and CRJs to MEM, and DL has a large operation at BOS, so you can still earn EQM that way. Also VS to LHR, AZ to MXP (and, seasonally, FCO), and AF to CDG. The transcon situation will be improved May 1 when Song goes away and DL transcons and nonstops to Florida earn CO EQM again.