Catchup payment for lapsed subscriptions

If a members subscription expired say 2 weeks ago and they login today and renew, will this take in to account the last two weeks and then add on the normal rate/length?

Only if you configured renewals to extend from expiration date instead of payment date. By default a "gap" is created in their subscription as it starts their renewal on the date they paid. This is configured within CBSubs > Plans > YOUR_PLAN > Pricing by adjusting the "Manual renewal extends expiration date as follows" parameter. Note this doesn't consider how far back their expiration date was. So if it was 2 years ago they'd have to pay 2 years to catch up.

I don't understand which one will force a catch-up payment and then a normal sub fee. The wording is unclear.   

eg : if the member sub expired 2 weeks ago and they resub today there is two weeks back fees owing along with the normal fee.

You would set it so renewal starts at expiration date if you want to force them to pay for the gap that they were expired for. So their renewal would start when they expired not when they paid. The only way to add a fee based off a gap is probably CBSubs Promotions since it can modify prices negatively and positively.

So option "Renewal starts at expiration date or at payment date - whichever happens first (allow overlap but no free gap)" will do this? I think maybe this could a little clearer.

No, that would allow overlap. What you're looking for is "Renewal extends expiration date (without gap or overlap)". Their renewal would always extend from their expiration date.

So if they expired 2 weeks ago their subscription, when renewed, would have a start date of 2 weeks ago and its expiration date would be calculated from that. Effectively they have to pay for those 2 weeks, but it's not done as a fee it's just done as the start point of their subscription renewal. So if the plan is 1 month duration they're still paying for just 1 month, but it's starting from 2 weeks ago.