i am setting manager account for my share business . i short sell a share for example (ABC_APR) 1000 share , with the strategy that i will re purchase it in the future .
Now i have a problem how to settle my this transaction in my manager account . as i generated a sale , it is showing my (-1000 ) share and with avg cost 0 , in my inventery section
You are selling your share - you are buying an option to sell it,
Average cost is calculated from Purchases (not Sales) as it gets transferred to the P&L as the expense which is related to a sale. So the question is, when are you recognising the revenue from the short sell? At the short sell point or upon the repurchase.
Short selling a share and buying a “Put” option to sell are two different things
Purchasing a PUT OPTION and entering into a SHORT SELLING transaction are the two most common ways for traders to profit when the price of an underlying asset decreases, but the payoffs are quite different.
Even though both of these instruments appreciate in value when the price of the underlying asset decreases, the amount of loss and pain incurred by the holder of each position when the price of the underlying asset increases is drastically different. This is because the short sell transaction obligates the trader to perform a specific action while the put option transaction only gives the trader the right to do so.
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With a short sale, an investor borrows shares from a broker and sells them on the market, hoping the price has decreased so they can buy them back at a lower cost. If the price has risen, they lose money.
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Buying a put option allows an investor to benefit from a drop in the price of the underlying asset, while also limiting how much loss they may sustain if the price rises.
Sorry, my reply above was wrong
What I meant, as Brucanna spelled out, selling a share short implies borrowing a share and then selling it. So you have to acquire the asset before selling it. You will have a liability on your balance sheet representing the share you have to pay back and the proceeds of the share sale in your bank account
How will we configure it all this in our manager accounting system
If you want to account for trading shares then I am not convinced that Manager is the right platform. You really need a software package which will track the different assets and mark them to market daily or else you will have a false sense of security
It would be possible to do this in Manager but would require a lot of accounting and investment knowledge
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It is not complicated at all using Manager, read these topics as a start:
https://forum.manager.io/t/can-manager-handle-investment-tracking/7819/5
https://forum.manager.io/t/market-adjustment-for-shares/8713/11
Also put “shares” into the search 
to find other topics
Shares are like other assets (real estate) you don’t adjust to market daily as market movements aren’t accounting transactions. For example, if you buy inventory at 2.00 each and the supplier changes the price to 1.50 or 2.50, then you don’t revalue your existing inventory, the same applies to shares.
For market valuations, use your account with the broker.