Two important things to note:
1. 2FA wallets use a special seed that are unique to Electrum 2FA wallets (and detected by the application as such). The seeds are "special" because they actually generate 3 different master private keys. The first gets put into the wallet file, the second is "hidden" unless you disable 2FA functionality when restoring and the third is owned by TrustedCoin. The result is that you cannot, as far as I'm aware, use custom seeds for Electrum 2FA wallets.
2. 2FA wallets will charge you extra fees for the 2FA service. You have to "prepay" for 20 or 100 transaction credits, 0.002 or 0.005 BTC respectively. (read more here:
https://api.trustedcoin.com/#/electrum-help) These charges are ADDITIONAL to the normal bitcoin transaction fees.
If you want to use a custom seed, you can only use it with a "standard" wallet.