There are a couple of answers to this question.
Firstly, you can have 'protected rights' on authorisations held prior to June 1st. These can be added to a JAR 66 licence but there may be restrictions (say if you were only a & c under section L), then your JAR 66 licence would show limitations on the types on your licence. This is providing, on your licence conversion, your QA dept submitted the standard letter format the CAA have requested. All QA depts should be aware of this.
Second part: For new 66 type ratings (on your 66 licence) the course must have been presented by a JAR 147 organisation that is approved to teach the requisite course. You can only apply for a 66 type rating against a manufacturers course (manufacturers cannot apply for JAR 147 at this time!) if the course has been audited by a JAR 145 organisation and that 145 organisation verifies the course content is appropriate to the 66 licence requirements. (This has serious implications for organisations such as 'flightsafety international' who do training on behalf of manufacturers but are not JAR 147 approved.)Only when the type rating is endorsed on your 66 licence can the QA dept of a JAR 145 grant company authorisation on the aircraft type they wish you to work on.
Hope this helps, I believe it to be the current situation but Roy Burdon at CAA Gatwick is the man with all the answers !!