I never really had too much trouble with keywords across both catalogues, generally with those there wasn't much crossover. Although I do put a lot of effort into keywording my images I think I need to do a bit of research into managing keywords efficiently, and also improving applying them to images. After my last two day airshow I had around 5000 images to keyword with aircraft types, display teams and some other details. Many images have more than one type of aircraft, in one part of the display there was a formation of 13 Spitfires, all of different marks, sorting out which was which was a pretty intensive job, that can really only be done manually by someone who knows the subject matter.
One thing I do use, and is really good for separating general groups of images are IPTC subject codes. If you follow the link you will find a page that will allow you to find the correct subject codes. I use the correct codes, but if you are not going to embed that data in the EXIF of exported images, and just use it as a identifier within Lr you could make up your own codes. In Lr you can use multiple codes, you just separate them with a comma just like with keywords. You can use them in creating Smart Collections though, so they can be really handy. For me using the codes means that I'm not having to try and separate different genres of images solely by keywords.