If you are not staying in the same exact hotel, I'd not expect much of a break; that's what the loyalty programs are for, and you'd be best off picking a loyalty program and sticking with it instead of jumping around. The question of "which program is best" really depends on a lot of factors: price range, expected amenities, what benefits you want to gain, city, etc.

If you'll be in the same city for the duration, I'd book several one-night stays at various properties, to get a feel for each; I'd not want to work out a nice deal on a mediocre hotel because then I'm stuck there for 8 weeks. As you stay in each one, speak to the hotel manager directly. Emailing and calling are also effective but an in-person visit can often be more productive. Tell them you are looking at X, Y and Z other hotels and ask them what they can offer you for an expected 90 nights in the next 120 days (or whatever your numbers are). I find that hotel managers respond better when there is an actual number of room nights attached--- the phrase "room nights" is one of their big metrics so if you walk in speaking their language, it tends to get their attention.

Also know what is reasonable to expect in the area you are visiting before you walk in. If you're looking for an $89/night rate for 90 days in downtown Boston, you won't find it. Think of some non-discount benefits you could also accept. The manager may only be able to come down 25% on the room price but may be willing to give you a $100 weekly food and beverage credit, or maybe they will offer you use of their hotel shuttle during hours when it doesn't normally run, hence saving you the expense of a rental car. Ask them if they have sister properties in that city which may offer a lower long-term rate. Walk in with lots of questions and lots of suggestions--- the worst they can do is say No.