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I've solved all the normal clues, have the theme, know what I'm meant to do - but am totally stuck with the last three. Would appreciate help of any kind with these two.
16 A. These hold burning matches left in boxes (9) l?ns
12 D. Sports car's base is tangled up with tree (9) re?s

NB. This is a themed crossword and groups of letters (which are all flowers or plants) are removed from the answers above - that's why the length given doesn't match.The completed cells don't necessarily spell a word - 'wasters' would be entered as 'ws' for example. I've been scouring lists for five-letter words which could be fitted into the answers above, but have got nowhere.

Why 5 letter words?

The answers to both clues are given as 9 letters, but there are only 4 spaces in each - so a five-letter word has been taken out.

I'm probably being really stupid but it looks as though 6 are missing as you give 3 letters each time and there are supposed to be 9 altogether.

Sorry, if I've set it out badly - I see what you mean!
Basically, there's a 5-letter word(a flower or plant) somewhere inside the 9-letter word which is the answer to the actual clue. The blank spaces I have shown(?) are part of the answer (to the clue), NOT part of the 5-letter word which has been removed.
I was hoping someone could answer the clue and I could spot the 5-letter word inside it.

The first one is LINSTOCKS (which are "staffs to hold a lighted match for firing a cannon").

It fits the clue L(eft)IN STOCKS (one meaning of which is boxes) and the five letter plant / flower to take out is STOCK

Thanks, Brackendale - a terrific help.I'll have another go at 12 D. now.

I've got the family and the computer trying to crack the other one (12 Down) but without success.

Have you made any progress, Chips?

Thanks,Brackendale - I haven't made any progress with 12 D, but I've been working on it for hours. I've tried breaking down the clue a bit more - spending time on 'sports' as in 'wears' , as well as sports/games. I thought there might be an anagram of 'cars base'+tree (trying elm,fir etc). There are too many 9-letter words with 're?s' in them somewhere. I'll soldier on a bit longer.

12d is an anagram. E is "the base of the natural system of logarithms". So CARS+E+TREE anagrammed = RECREATES.