You have a much bigger challenge than placing the (R)! :-)
What does/will the logo look like?

hhp

Well. Our creative director decided not to spend alot of time on it and just to match it with one of the fonts we have.
It is for a local farm products.

Hmmm.
If you're open to a crit on the logo please let us/me know.

hhp

This isn't something that the designer should decide; your client or their lawyer should tell you which mark(s) to use.

I'm not a lawyer but my guess is that you can't use the registration mark on the new version because it can only be used after the government registers a mark, not while the application is pending. You'd probably have to use TM or SM instead. (I'm assuming that the new version will require going through the registration process again.)

The government FAQ page below might be helpful:
http://www.uspto.gov/faq/trademarks.jsp#_Toc275426682

@ hrant:
Of course I am :)

@ James: I understand. As you mentioned, yes we won't use the mark now, but we're printing labels for internal communication. Later on, we'll have to place the R mark :)

> Later on, we'll have to place the R mark

Well, as I mentioned you may have to use TM or SM at first. The circle R cannot be used until the new mark is registered and approved with the trademark office.

In the second word, you have a kashida (elongation) in an invalid position according to traditional script grammar. You can't insert a kashida before a final jim. The only legitimate place in that word for a kashida is between the medial khah and lam: الخـــليج

Personally, I would avoid kashidas altogether in this word mark: they're unnecessary and make the Arabic less harmonious with the Latin. If I were to use one at all, it would be only in the first word, as you have it, after the initial mim.

I'm not as knowledgeable as John concerning the traditional rules of kasheeda placement, but even if I were I might actually shoot for -what must be- a superset of those rules: if it looks good, it is good. However, in this case at least it doesn't. :-/ You could make the kasheeda in the first word longer to end up with a nice symmetry, but I would actually agree with John that -at least in this case- no kasheedas at all might be best, especially considering the Latin is so dense.

Speaking of the Latin, there's something funny about it - it's like a distorted Futura. It's pudgy, and the spacing is very uneven. Also, the Latin is rather conventional while the Arabic is somewhat progressive (especially that 'ayn).

Then there's the problem of apparent size/importance (marginally related to kasheeda inclusions). By being both smaller and lighter the Arabic seems far less important. On the other hand this logo might need that feature - it's hard to know from the outside.

Concerning your original question, I'd suggest trying something that many designers would consider gimmicky: try making the dot of the jeem coincide with the dot of the "i", and make that the (R) sign! You might have to make the Arabic longer/bigger, but for one thing that would address the apparent importance issue above.

Lastly, the dots of the yaa' aren't sitting happy in relation to the "el".

hhp

*blink* *blink* Why did I suddenly see the arabic text in blue with red dots? I didn't hit my head or anything...

Thank you all for your constructive ctiricque
Here's the new logo. It is already approved. But I would love to get your feedback for future projects :)

@ Te: I think because it is RGB :)