Do you mean that booking with AA to Munich you only get points to the European city where you'd change planes, say London, but no AA points for the London-Munich portion on the partner?
AA and partners can be a very intimidating experience. Depending on the fare class for the partner, you could get ZERO, 25%, 30%, 50%, or even full miles. Here is a link to the partners page if you want to look at how it all works out:
http://www.aa.com/aa/i18nForward.do?...lines/main.jsp
You would get full miles for the AA flight to London, and then 25% for a BA connecting flight. The AA wiki on FT spells a lot of the fine print out:
http://www.flyerguide.com/wiki/index...rican_Airlines
There is a workaround (book the AA codeshare London-Munich, though it may cost more).
One thing you need to consider, if travel will exceed 100K a year and that is ongoing, is upgrades. Both UA and AA offer systemwide upgrades for international travel when you reach that 100K mark (6 at UA, 8 at AA). Lifetime status is also accrued differently on either carrier (AA allows miles from all sources while UA requires flights on UA metal).
Don't rush into any decisions. Take some time to read about the carriers on their own web sites, too.